This little shit and his family discovers your party trying to be stealthy about an hour's walk from his village...

This. If some villagers are found murdered in the woods and some murderhobos came through at the same time, it's pretty obvious who killed them.

>if they kill them there's a chance it'll ruin their reputation

I'm not actually sure if my players care enough about their reputation to put it above finishing a mission.

Talk to them all, demonstrate good will, ask what their grievances are and attempt to address them to the extent morally allowable. If their goals are evil, detain them, and execute those who have committed crimes and will not repent. Deliver those who have not comitted crimes but conspire to do so to authorities who will treat them appropriately. Release all others, as they are innocent.

We shall brook no immoral actions, neither from others nor from ourselves.

Hold them captive somewhere hidden until goal has been achieved. A good adventuring party should have more than enough rope to restrain them. Quest successful and reputation untarnished.

And if they don't speak Common or any language you know on hand?

Of course, then you have to risk revealing yourself to find the hidden place, leave someone there to guard them or risk having them die from the cold or from beasts.

Brutally murder the whole family, except the weakest son. Leave him tied up, too maimed to ever be a threat, and let him tell stories of your ferocity when his friends find him. You'll be long gone before trouble happens, and if people start thinking you're an outlaw, do some random do-goodery for the local attention whore to make things seem better.

Compromise the Mission? Yeah that's not gonna fly. Yeah I could mind control them, but it's not exactly fullproof. Missing villagers in a violence strewn area? not that strange really. Sucks to be them.

Not as many as you'd think, and anyway it's a trope.
Remember Usagi Yojimbo? Ninjas try to 'kill the whole village, leaving no witnesses' every few issues.
The party might have issues with becoming the bad guys, tho. Maybe they should start wearing a uniform with skull designs, tres chic.

Use rope or duct tape. Someone will find them later. It isn't my problem so long as they are tied and gagged. Or just kill 'em and hide the bodies well.

They really should've slit his throat.

>And if they don't speak Common or any language you know on hand?
Then why the fuck are you working in this region? If you're doing serious stuff in foreign lands you should have a translator.
A party without one probably wouldn't care about reputation anyway. But they would also pretty much deserve to get caught for their lack of foresight and preparation.

In my game, I don't care about a good reputation. Hell, a reputation for murdering the everloving fuck out of everyone who opposes me or aids those who oppose me is a net plus - to be fair, I balance this with carrots for those who do my bidding. My DM has to reward me to not do that for its own sake.

We're playing Pathfinder with tier one classes. Stuff them in a pocket dimension until the mission, whatever it is, is completed, then let them out with no harm done. Maybe give them a couple hundred gold for their troubles, and a warning not to meddle in the affairs of wizards again.

Oooh, the terrible wrath of brown people. What are they going to do, NOT rape Dietrich's wife?

Just napalm their village and be done with it. You can always find a new village.

You mean like that one World War 2 movie about people with feet fetish or something?