Yes indeed^^
Personally, i would very much favour that the faction leaderships and the dev team crash their heads together as a sort of comitee to agree on more or less iffy things, maybe a voted commitee would be another option.
If the common sense and goodwill approach fails(most likely) i would put in some hardcoded rules.
Like this: each faction is forced to check if any ally or friendly (not neutral) is also allied or friendly with its enemies. All these should be nixed, to level the field - leaving the ally of a only the option of being neutral or worse to the enemy of his ally.
After that, i would propose to hand out the "grey areal allowings" as in either giving each faction the right to have one "irregular" ally, or more upon dev/comitee approvement.
If done sensibly this shouldn't change much for many factions other then giving the time to rethink if maybe a trade partner is just a mere "neutral" thing instead of an ally...ore for the worse offenders if it is really possible to be friends with everyone minus Nomads.
This is not a very refind system but a quick way to bring out the trash and breathe some fresh air into things (after all, diplo changes could and should be rp able and so on..)