Yes I agree that atomism was identified as the threat to be destroyed, but not so much just because it wasn't water, or fire, but because atoms weren't as easy to make DIVINE. The stoics had no problem reconciling fire with divinity. I suppose you could say (as many do now) that god(s) created the atoms, but it sounds like the religionists identified atoms as more of a threat, even though Democritus himself was a strict determinist, which would have made his views more religious-compatible.
Maybe adding on the swerve made Epicurus more of a potent threat than Democritean atomism.