So I'm not precisely sure where I went wrong, but Markarth is pretty much unplayable for me. I got to the city via the jail, as I got a fine for fighting some Stormcloaks. Since I was so close to the palace, I just went there and cleared out the ruins, met that girl in the Halls of the Dead, and started quest for the Thalmor patrolling in front of the Jarl.

There, the Forsworn Conspiracy started. Now, I don't know if this might have caused the bug or not, but I attacked the Forsworn before he attacked me, though it was after he had killed the girl. Also I took her clothes. It seems that after I did this, there are many random people who are now hostile towards me. The Vigilant was hostile until I met that dude at the Shrine of Talos. I went and started the Molag Bal chain after I left the Shrine. When I then went to turn in my quest with the Thalmor, all three of them were hostile, as well as the Jarl, his steward and his housecarl.

Then I thought, well, maybe I just have to complete this questline. I investigated the murdered girl, Margaret, and then I went to the Treasury to investigate the Silver-Bloods. As soon as I entered, a female Silver-Blood started attacking me, though I just ignored it as I had eventually ignored the Vigilant's attacks. However when I got to the room with the guy I was supposed to talk to, he was also immediately hostile and attacked me. He's unkillable, at least at this stage of the quest, and of course does not give up fighting.

I'm not really sure what to do. I've been looking around but I haven't seen any discussion about hostilities so early in the questline, so I figured I would put this up. I'm basically stuck between leaving Markarth and hoping that some patch comes out to fix this, or reloading to 4 hours before my last autosave, and losing clearing out those ruins as well as the Northwatch Keep. Any suggestions?