If you think the issue that makes this strategy so viable is how friendly alchemists are to BD, and then how easily he can change teams late-game, then there’s a simple fix:
Give him equal helping and kill potential to make him more dangerous. This can be done by giving him limited healing potions, specifically 3, and upping the bombs to 3 also. That way he poses equal aid and threat to both sides, as he can only help BD so much with only 3 heals, but also can easily knock out unseen/cult with 3 bombs. Also should consider dropping the stoneskin potions down to 2 or 3, so that he can’t just sleep on those for the whole game, and actually has to placate himself to both sides to avoid getting killed on nights he doesn’t have stoneskin.