Do Elves ever forget a murder?
Ok, problem solved. I traveled back to Whiterun, slept there for 24h then went back to Markarth. Now the elves aren't hostile. That amout of time was enough, appearantely. The murdered guard hasn't respawned. Looks like its possible to get rid of the elves in the Underkeep. Probbably gonna do that, for RP reasons.