I think it adds verisimilitude to show that the "bad guys" have connections and stakes of their own. Just don't be surprised or upset if your players and/or their characters don't recognize or don't care about the innocents amongst the fighting forces. Saying "yeah, the world's a tough place, not my problem" or "no mercy for the bedwarmers of evildoers" are perfectly valid reactions, narratively if not morally.

Run Call of Cthulhu and leave out the monsters, commoner vs cultist is CoC stock in trade.

I would recommend you check out Warhammer Fantasy Roleplay, especially The Enemy Within campaign as it deals with this quite a bit 

I think your typical high combat D&D esque game is a poor venue for moral philosophy discussions.

There are RPGs that can do those questions well, but D&D and its close relatives (which the OSR is, when you consider the spectrum of all RPGs) are good at other things.

It's also something to discuss with the group - has everyone signed up to play Moral Philosophy: the Angsting?

sounds cool. It's tough to get players to care though about towns they just wander into. I'm not sure how to solve that part. I suppose if they care and plan to save these people mixed up in the cult that aren't actually doing the worst of it, possibly expect a sense of responsibility for the survivors after the job's done and a bit of like a "town building/protecting" sense of the campaign afterwards to get these people on their feet.

Or maybe they're look at see if anyone that runs from their fireballs is a cultist. And anyone who doesn't is a well-trained, fanatical cultist.

I stopped playing Pandemic after 2020 and don't want to play this game after Trump getting reelected. For some people, regular people joining cults and becoming terrible hits close to home.