• Ira (and, depending on your cynical political view on the world and Arulco, common sense) suggests that the US is propping up the Deidranna regime. Considering the regime is in power for about a decade, based in middle america and the US hasn't intervened in any way, it's likely they'd like it to stay... which makes them antagonistic to you. Piss them off enough, and they will feel the need to do something about you...
  Expropriating Doreen, a US entrepreneur, is a grave violation of international treaties.
  Doreen is a US citizen. Killing her is clearly a terror act.
  Hurting of possibly even killing the Kulbas is clearly a terror act. It does not matter who kills them - you removed them from Chitzena by force, and you are thus responsible for their wellbeing.
  Recruiting convicted criminals makes you more despicable. This can both apply to Shank & Dynamo as well as Reuban and Jimmy.
  Working together with internationally sought terrorists (Slay)? You know how those people end, do you?
  Recruiting barely concealed russian soldiers won't make them friendlier.
  Close relations to socialist states are suspicious.
  Close relations to criminal organisations are damning.
  Evacuating the Kulbas out of a warzone will positively surprise the US.
  The resurfacing of an aid worker thought lost is inconvenient, but better than nothing.
  
  If you are on good terms with the US, the US will do nothing. That's the best you can hope for.
  On bad terms, they could press for sanctions against you. Perhaps you will then have to look for other buyers for your silver, resulting in -x% mine income... perhaps BR deliveries would be delayed. Restricting MERC & AIM would be logical, but absolutely game breaking.
  Direct military intervention would be absolutely game-breaking, so I guess not. I see no way the player could realistically survive the US attacking. Nope.
  
• Russia is only present in Arulco by a few mercenaries it sent there to train the Arulco army (Conrad & Iggy), possibly to not entirely leave the country to the US. Their main interest here was mainly to force the US to commit resources themselves.
  Killing Conrad & Iggy will make them hostile to you nonetheless.
  By recruiting Conrad & Iggy, this could actually put them on the winning side... that's a bonus.
  
  On very good terms, they might use their veto power to block US sanctions against you.
  On bad terms, they might join sanctions against you.
  
• The eastern-european mafia. Kingpin is bound to have outside connections, no?
  Any move against Kingpin is a move against the mafia. They dislike having to replace their people.
  Getting on good terms with Kingping gets you on good terms with the too.
  
  On good terms, they might find a way to give you a small discount at your favourite mob-based weapon dealer.
  On bad terms, Tony might demand a risk surcharge.
  On very bad terms... well, the mafia might have more than just 6 hitmen, no? Who knows, they might even send more than one per time.
  
• The southernamerican socialist state of, I don't know, Venezuela would like to see the capitalist, american puppet Deidranna disempowered sooner than later. Thus they are in principle very friendly to you, altough all these foreign capitalist mercenaries are worrying.
  Recruiting the rebels is definitely positive.
  Completing the food quest shows your commitment to the people.
  Expropriating Doreen, who is all but a slaver, and giving production facilities back to the people is the right revolutionary spirit.
  Liberating those imprisoned by the regime is positive.
  Marrying women off against their will is a troubling development.
  Killing an entire extended farmer family is very troubling, and shows you are still bound to business interest.
  Hiring outside mercenaries, who work for money and not for the cause, is bad
  Bringing in masses of outside footsoldiers (Kerberus) might derail the revolution.
  Close relations to capitalist states are suspicious.
  
  On good terms, they might occasionally offer you free but inexperienced volunteers (green militia).
  
• The WHO is involved in Arulco due to the cathastrophic health system. They are grateful if you help them, but won't tolerate human rights violations.
  Helping the few local doctors earns their goodwill.
  Combating disease and curing the population helps tremendously.
  Attacking hospitals, their staff and patients is a human rights violation.
  Beheading people in the streets? Executing civilians because you suspect them to be a 'terrorist' without trail? What kind of monster are you?
  
  On good terms, they might occasionally send you spare medical supplies.
  On bad terms, their disease info service costs a lot more.
  
• Interpol is looking for some well-known terrorists in Arulco, and welcomes any help in that regard.
  Having terrorists brought to justice (with proof!) is a good thing.
  Killing their contacts, however, isn't.
  Recruiting those terrorists instead is unacceptable.
  
  On good terms, they might give you some intel... and reveal the location of all enemy generals on the map. Because they probably committed war crimes or sth.
  On bad terms, they... hmmm... put you on their wanted list. Not that it matters in Arulco (does it?).
  
• The catholic church, while not as powerful as they once were (thank god for that!), still have a lot of money an influence...
  Stealing from their church, damaging their property, or attacking their members is frowned upon.
  They only know you from Father. Help him, and he'll put in a good word for you
  (New quest solution idea) A relic like the chalice should be in the hands of the church.
  
  Hmm. I got nothing here.
  
• The WWF (no, not that one) would like you to not eradicate endangered species, thank you.
  I said not eradicate. How thick are you?
  And no, trading animal parts is also bad.
  
  On bad terms... I don't know. They start a twitter campaign against you?
  
• (AIMNAS-only) Perhaps some modder might place a drug farm in one of his maps. Arulco is pretty far off, labour is cheap... a drug cartel might have a factory here.
  Wiping out the entire cartel's Arulco branch might, ahem, sour the relations.
  (Possible optional quest idea) The cartel might contact you after taking over their lab and offer you a deal: you operate the lab from now on and protect it, and they might look past your previous actions (what else are they going to do anway?). Perhaps they even give you a part of the profits.
  
  There might even be additional work for a cartel to be done, which would alter other relations.
  
  On good terms, well, money.
  On bad terms, well, cartel hitmen.

This would let the US take active military actions when they get really, really annoyed with you, but avoid any game-breaking amphibious invasions. Any thoughts?

The problem with US covert squads is that there is no realistic need for the US to be covert in the first place. They have no reason to hide from the player, while the player has all reasons to hide from them. And if the player would dare to attack their forces, all hell would break loose. An US airstrike would simply eradicate an entire sector, without any chance to defend or retaliate. All you could do is move into the underground caves.

That said, the General in Alma is American, and it stands to reason plenty of the blackshirts are either advisers, contractors, or mercs allowed to work for the Arulcan government by the US in some form or another (the DoD, State Dept, and Intel agencies allowed it).

• Ricci Mining Corp. are, as jasmith pointed out, one of the main backers of Deidranna, which automatically makes them antagonistic towards the rebels.
  Extorting money from members of the Ricci family itself seems like sure way to piss them off.
  Killing members of the family is will let them go ballistic.
  
  Lorewise, the bad stuff would come in UB. For now, they could harm your mining efforts in some way - perhaps blocking routes to get the ore out of country, effectively lowering kine income.
• There might be some former officer corps in Alma. This represents family of the army brass and retired officers - people you don't gun down on the battlefield, but who are nevertheless closely tied to the army and might still have some draw in Alma.
  Executing highranking officers will make them angry (for gameplay reasons, this refers to NPCs like the Lt. and the General, which you do not have to gun down in the campaign).
  Dynamo is a known malcontent in Alma. Freeing him and bringing him back will not sit well with all of Alma...
  The army has been fighting the rebels for a long time. Miguel, Carlos and Manuel did make a few widows, which makes anybody working with them unwelcome.
  Assassinating the generals, who are members of this group, won't make them friendlier.
  Bandaging the Lt. is a sign of goodwill.
  If you allow the Lt. to walk free, he will indeed lay in a good word, improving relations.
  Granting former army personnel access to your inner circle shows them that they don't have to go down with Deidranna.
  
  These people know the inner workings of the army like nobody else. They could provide you with info on army patrols, military installations etc.. They could also point out army storage facilities you do not yet know about.
  These people run the city. They won't openly rebel, but don't expect loyalty to be high... or the prison to run well against their will.
  If any group were to infiltrate your militia with assassins, these would be the guys.
• Arulco isn't exactly known for its sophisticated technological sector. In fact, an outside arms developer uses the remote country for a secret experimental weapons program in Orta. In exchange for secrecy and protection, the royal army gets a few special toys for its elite divisions (the rocket rifles).
  They won't be happy if you steal a working prototype from Alma.
  They will be even less happy if you help yourself to a whole cache of the things.
  They won't be happy if you threaten or even kill their top scientists.
  They will be extremely pissed if you raid their main lab.
  Dr. Kairns has gone rogue. If he works for you, that will look bad in their quarterly performance review.
  The robot is another prototype of theirs. You aren't even supposed to know about that, stop using their stuff!
  If Dr. Kairns were to quietly vanish, that would solve an embarassing security glitch.
  That robot also needs to go.
  If you bribe one of their scientists, he might be able to make you look not as bad.
  
  If you really get on their nerves, they might increase their deliveries to the army, to get you out of the way. Better gear for the army? (might be detrimental, as we get whatever the army carries by killing them anyway)
  If we are not too much a pest, they might just cut their losses and leave the country, which means less hightech for the army.
• Harrows clothing Inc. produces stylish clothes. Their 'by kids, for kids' T-Shirt line is extremely popular with teens nowadays.
  Shooting their CEO in the head sure won't get you a discount, that's for sure.
  Threatening the company with violence to leave the country is no style to lead a business.
  Convincing their CEO that the country is a warzone and that they should leave, while also pointing out a few technical labour law violations, might make them antagonistic in the short run. But as you turn the country into rubble, they might realisz that leaving was the smart thing to do.
  
  If you harm or threaten Doreen, but she manages to leave the country, will result in some very bad press back in the states. This will affect your standing with other organisations negatively.
  If you make Doreen realize the error of her ways, and allow her to leave unharmed, she might actually result in some good press, by pointing out how you are not as bad as other reports indicate.
  Free T-Shirts?
• The UK can be for or against sanction too, like the US and Russia. They don't have many interests here, but...
  Mickey O'Brien and Devin Connell are not only arms dealers/smugglers of the worst kind, they also have a history of armed conflict with the UK that goes back a few decades. Details are not important for you, but your dealings with them will be monitored.
  The druggist is also of special interest here.
  
  They can affect sanctions positively or negatively.