I have never been able to use a disguise to save myself from a faction that hated me, the only thing it does is break the Reputation system and give you a "shoot on sight" rep with factions opposite your own.

Not really.

Dont use them

I never use disguises either I never really saw the point. I just go in guns blazing if I have to enter an enemy base.

I don't use them often, since rangers and mongrels can see through them.