So that means it was pointless for me to set up my weapons of the east vs west modes, giving the enemy one type of weapon and militia another type. If that is the case my militia won't drop their weapons?

If so, that kinda is a bummer.

Assuming you are using base 1.13, in your "data-1.13" folder open "JA2_options.ini"

;------------------------------------------------------------------------------------------------------------------------------
; This setting determines whether militia can drop their equipment when they die, like enemies do.
;
; 0 = JA2 Default. Militia can't drop any equipment.
; 1 = Militia can drop equipment only if they've been killed by enemies/civilians/other militia (but not by mercs!)
; 2 = Militia can drop their equipment regardless of who killed them.
;
; The "ENEMIES DROP ALL" ingame options-menu setting affects the items dropped by militia just like it does for enemies. When 
; turned on, Militia will drop everything they're carrying. When turned off, they'll drop their equipment randomly 
; (or none at all).
;------------------------------------------------------------------------------------------------------------------------------

MILITIA_DROP_EQUIPMENT = 2