If you have firepots then you can just do some faction work to even out your foul deeds.
Get wooden shards from this quest:
https://wiki.project1999.com/Trueshot_Longbow_Quest
Turn them in with this quest:
https://wiki.project1999.com/Peacekeeper_Staff_Quest
This of course assumes that all the negative factions from killing the guards are raised by the wooden shards turn in. I think they are but I haven't killed guards so I can't be sure (just going off the wiki). But you can just max out guard faction with the quest, then kill down to apprehensive and cycle this till you max heretics faction.
Also skeleton illusion does help your faction.