Here's the fix:
- Walk into Markath, weapons sheathed, so the guard will talk to you.
- When he's finished, and the dialog options pop up, open the console (button above tab).
- Click his head, and his hex code will appear. Then type "paycrimegold" into the console.
- You'll hear a coin noise, and your bounty will be removed from your cash pile. (it can be over 10k, mine was only 2500 or so).
- Leave the city, wander around the guards a bit, a coupla might talk to you, just tab out and they'll leave you alone.
- When you reenter, they'll aggro towards your follower, but will behave like normal towards you.
As I said, a few of the guards will still be glitched, and you'll have to go through the conversation once to fix it.
Oh, and here's a screenshot of a dragon that attacked Riverwood (the starting town) and killed my favourite blacksmith :(