A sad truth about writing the bad guys

I was all set to make my villains torch-and-pitchfork-because-of-fear villagers, because I liked the idea of my novel having antagonists but not any conventional villains. (This would be my next novel; the one I'm working on does have conventional tear-your-entrails-out-because-it's-fun villains. I'm trying to change things up, yo.)

Great idea, right? Of course! Awesome! Bring on the unconventionality! And then I realized that if I do that I have two problems. Two fairly big problems:

1) Unless I have the protagonist kill them all, they have no reason to stop coming after him*, and this isn't the kind of story where the actually-friendly protagonist will have time or opportunity to convince anyone of his good intentions. Which makes the happy ending problematic.

2) If I have the protagonist kill them all, he won't be the protagonist so much as a mass murderer. Which makes a happy ending impossible.

Oops.

Luckily, I have another idea! Sort of! I just wanted to share my useless doubtlessly fascinating insight. Now I need to motivate the bad guys.

*(my plan is to send this one to Dreamspinner Press, and they only take books with male protagonists. The novel I'm currently revising stars a woman. Yes, I felt the need to mention that.)

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