If a faction is neutral then of course members signing up for whom they please is natural, but if a faction is trying to be friendly (or allied) with another then you better have no members signing up against. Anything els is a lack of competence and control by the leadership involved, making said faction a liability.
That would be true if playing in a Strategus battle wasn't primarily about the personal benefits--namely, tons of fun, and loads of experience so you can retire fifteen times and get those masterwork smoke bombs you wanted so much.
It might be more important if you think the FCC birds are so much more talented than anyone else who fights that they are measured on a different scale, but that's an unreasonable approach to diplomacy, and most of them do, actually, die sometimes. I've seen it myself. In that case, though, you can't make the
categorical claim that factions need to control their members when they're "friendly" (whatever the hell that means) with another faction, and you're picking on FCC.
In the case of an explicit public alliance, factions are essentially fighting as one faction, so it would make sense for the members of each faction only to sign up for their own side, but you should not assume that, "We do not hate you," means, "We will always fight for you and not your enemies."
(This is all completely restricted to mercenaries; obviously sending troops or goods or gold to the enemy would constitute aid.)