I still like your idea of the pheromones. That could be used as a true ending. Gives Sonic a "bad" guy to stop, a day saved, and a sexy reward for good behavior (if you went that route of course). Or like you said, have another ending where if you didn't meet a certain RWC, that you get a standard ending and never find out what's causing everyone to act weird. Vanilla comes home, business as usual.
Great One - True Ending (We find out why everyone is horny)
Good One - Vanilla comes back home. Her and Cream reward you together. (You leave suspicious, but say you will look into it later along with Amy)
A bad One - Vanilla comes back home. Kicks you out for being a bad babysitter with low alignment.
Terrible One - A knock at the door, but it isn't Vanilla like you expect. The Villain is at the door. No one is safe
Or.. just have one ending, Idk. Whatever's easier