Probably easiest to kill some elves and do some quests to raise THEIR faction a little (maybe do the quests first to give you some buffer faction to sacrifice to chase indigo brotherhood). If you only killed a couple enemies to go over the line, it won't really be much to get back to non KOS.
Here is one to kill (there are a couple in the swamp).
http://wiki.project1999.com/Jyle_Windstorm