Since the CS isn't out yet and I can't fix it with what I call the "sledgehammer approach" I need help from you people. Hopefully someone CAN help me.

What was supposed to do: Go to Karthwasten and brawl with the mercenary Atar so he leaves the mine and people alone.
What I did: Got there, spoke to the headman and, since I believed I shouldn't use forces because of what Farkas said to me (actually he meant don't KILL someone), gave Atar money to leave. Headman happy, Companion quest neither advancing nor has it been failed - it's still active, but Atar is gone.

Anyone got an idea how to solve this one? I hope if I could find Atar that I might still be able to trigger the relevant topic (brawl with him) since the quest is still active, else I managed to break the entire Companion quest line because I can't advance anymore. Would be really, really glad if someone got a solution.

I have exactly the same problem. It is possible to set the quest to the next stage using some console commands but I need the quest ID to do this... would be nice if someone knew how to find it.

You can look the quest up on UESPwiki. It shows the Quest ID on it's page.

to skip the quest "hired muscle".
Type player.setstage 00025231 100 and the game will finish the quest and give you 100g. You now can go to Skjor at Jorrvaskr who has a new quest for you.

If you need to fix another quest just type save fred 1 and wait for the notepad to popup. Now you can serarch with ctrl+f for the specified ID.

Getting in a fist-fight with the guy finishes the quest without killing him.

Thanks a lot, that was it.