It would be nice, and I think we've asked for it in the past, to have the ability to flag any mob for any 'alliance'.
In other words, if you wanted a group of Klingons to be friendly to a Federation player, you would flag them as 'Federation' instead of their default 'Klingon' alliance. That way they still use all their native attacks (not just reskinned Feds shooting phasers) against other non-Federation targets - even other Klingons.
It sure would save a lot of time having to re-costume mobs AND give a better, more realistic outcome/visual effect since they would be using their 'real' weapon types for their race.
I don't think the engine is set up to have factions dynamically change their allegence. I think the devs, when the want to make say KDF fight Gorn, have to create a new faction that looks and behaves like traditional Gorn except allegence.
If they were to attempt to implement this into the Foundry, it would most likely be them creating a multitude of factions with all the different possible combinations than could be.