I finished Cihdna mine quest and I attacked a few guards. Now The guards attack me with no option to pay my bounty or go to jail. Is there any way to make them stop or do I have to kill all of them every time I go to Markarth?

yield to the guard (put your weapon away) and go to jail, if its the quest im thinking off you need to do the jail thing

If you sided with the Forsworn I believe that the remaining Markath guards will be hostile. There is no way to alter those actions except for playing the quest over again.

I had the same extremely annoying bug happen to two of my games. A quick googling lead me to the discovery of the wonderful world of bug-busting console commands.

If you're on a PC, go in first person, hover your targeting reticle over a Markarth guard's head (the guide I read explicitly mentioned having the head within your reticle), and press the tilde key (~). A text box will appear at the bottom of your screen, type "Paycrimegold" without the quotation marks. If you're like me, and for a while you've just been slaughtering every guard in Markarth, the payment will be quite steep. In fact, I'm fairly certain that, should you not want to lose a ton of gold to a bug, you can drop the coin somewhere, and then pay the guard with the console command and it will only remove what's in your inv. I suspect this because I was carrying around 22k, with a few odd hundred and singles, and he took ALL of it, not a predefined incremental amount (1k, 2k, 3k etc.)

That fixed their aggression and looping of the quest text for me, hope it helps you.

Kinda convoluted but here is the fix that worked for me, with less steps. (For non PC users.)

http://www.youtube.com/watch?v=-dzCEkwX2VU

Actually here is what I did. I didn't kill the guards outside. I simply snuck in to the Shrine of Talos, killed the attacking guards, then I yielded, and started the dialogue tree like the link says.

I can now go back without the whole damn guard shift chasing me down.

I didn't have this problem. When I exited the prison and the forsworn attacked everyone, I just stood and watched. Then slowly walked down taking all the arrows from the guards bodies. I assume that as I didn't attack any guards with the forsworn, I didn't get a bounty.

I did the same thing just sat back and watched the battle and cleaned up the mess, I walked away free and clear so I thought. The Jarl even tells me he is sorry I was accused of the murders, but the next time I get busted for pickpocketing someone and get a 40gold bounty the guards want to toss me in the mines for the murders all over again so there is clearly a bug in the city. So I learned to keep a low profile in the city and save prior to committing any crimes as there is no way around the bug.

Bethesda forces player to avoid Markath, that skeeverhole of a city.
seems like everyone has to be a lawful citizen in markath then

Anyone knows if changing the jarl by siding with the stormcloaks is a legal means to reset the bounty?

I would be disappointed (but not surprised) if it doesn't, but logically since all the guards are replaced by stormcloaks and you are one of the top officers at the end of the quest line.