Murder has repercussions, how do I fix my reputation?
Solution 1:
The easiest way to improve reputation is to donate at temples. The other option would be to do certain quests, which influence reputation.
The wiki has a detailled cost breakdown for buying reputation up as well as a list of subquests influencing reputation.
As for the guards (flaming fist soldiers), they should disappear or become neutral, once your reputation recovered. But I cannot say for certain.