Ideally, I would keep the diplo penalty between good and evil civs, but remove or lessen the diplo
bonus between evil civs and other evil civs for rising AC. This represents the fact that while the basic conflict between good and evil gets more intense, the basic nature of evil - "evil turns on itself" - stays the same.
And as has been stated more than once, the only people with a vested interest in raising the AC are the Sheaim (especially when led by Os-Gabella) and, to a lesser extent, other civs following AV. A diplo penalty for ALL non-AV civs against AV followers - increasing as the AC rises - would not be out of line.
I would also change the nature of the mechanic specifically for the Plant civ, so that they would increase their hostility toward ALL other civs as the AV rises, since they believe that all other civs are destructive and "evil" by their standards. They certainly would not prefer evil civs over good ones - they likely
can not or
choose not to differentiate between them. The easiest way to simulate their contempt for everyone else - and wouldn't require re-coding of the AC mechanic - is simply to make them neutral, aggressive (not necessarily the civ trait, but the behavior) and to have a large starting penalty toward ALL other civs, in addition to other penalties (and bonuses) described above.
A couple of other ideas: I didn't see it mentioned above, but the Plant civ should probably be at peace with animals. They should be able to build various animal units (wolves perhaps as scouts or something, etc.). In that case, they might build the Grand Menagerie from humanoid slaves instead of animals.
They should automatically raze - or at least dramatically reduce the population of - all cities they conquer, perhaps spawning several units that have sprouted from the blood soaked into the soil and composting corpses of the slain - perhaps the number of spawns could depend on the lost population. Maybe even some sort of "plant zombie" controlled by some weird seed or something growing in the corpses that can control them!