After learning the "Bend Will" shout, I set off to cleanse each of the stones. However, while cleansing the Earth Stone, I had accidentally hit one of the NPCs with my spell. This caused all of the other NPCs to start attacking me. My follower decided to start killing them all, adding bounty. Not knowing what I should have done, I ran to the docks and got the hell back to Skyrim. If someone can tell me how I can remove my bounty on Raven Rock, that would be fantastic.

The simplest option would probably be to just load an earlier save.

load an earlier save or let yourself be arrested and pay the bounty in Raven Rock.

Load a earlier save, pay the bounty, or just go to jail(if they have jails. I've never been caught doing bad stuff in Raven Rock.) That's the only way you can do it without cheating.