Recently I have using the spell, dominate will on some shopkeepers and stealing their stuff on the process. The problem is they hate, when noticing my character they immediately attack me. So how can I fix this, will this negative reaction go away in time or is it permanent? Thanks.
I believe everyone who you use dominate will on hates you after the spell wears off, but I may be incorrect.
I'm pretty sure there's a way where if you tell a shopkeeper to back off (one of the F keys) and end the spell they'll hate you but not attack you. There may be more to it than this however and I can't easily find a thread that mentions it to reference, still a little experimentation would probably allow you to work out how to do it. Whatever hatred is gained is permanent however, so don't use it on people who give you quests unless you've already completed them.
If an NPC is scared and enters the "fleeing" mode, then you can still talk to them, but they will continue to hate you, and may attack you later, if/once they "build up their courage".