If you've only got the one molly, and he's a male, often the problem is that he's horny and frustrated, so he will pester everyone around. Options are to swap him for a female, or add 2-3 females (adding only one causes him to constantly pester just the one female, 2-3 spreads out his "attention"). Of course, adding any female mollies will also lead to them overpopulating like your guppies are working on... And adding only a female and removing the male usually doesn't change that, because usually the female is already preggers...
Alternatively, making sure there are lots of good hiding spaces and different areas where there can be territories can give the other fish the cover they need so they aren't being harassed by the molly. Make sure there are lots of spaces for a fish to dart into for cover.