I recently did the quest where I met the guy in the Temple of Talos in Markarth, after completing the quest I returned to the temple and found 4 guards who killed the quest giver guy and gave me the choice to go to prison or fight. I chose to fight them because I figured they were traitors for lack of a better word and killing them would give proof. After I killed all the guards in the temple I went outside and all the guards in the city came after me, so I then chose to go to prison. After I met with the main guy in there and we escaped I tried to return to Markarth on many ocaasions only to have all the guards confornt me and say, "You have committed crimes against Skyrim and her people, what say you." I try bribing them, doesn't work; I say take me to prison, and they say that they will but then they don't sheath their swords and then 1 second later it starts all over agian. I cannot walk more then 2 steps into the city and they will not take me to jail or let me pay a bounty. I cannot find a way to clear this so I can continue with the quests I have in Markarth which means I cannot advance in certain areas of the game. I refuse to restart especially after all the hours I have invested. What can I do to get rid of this obvious glitch? Please any help anyone can give will be greatly appreciated.

I would take this to the spoilers forum. I can smell a thread lock coming...

They never lock threads like this, they move them.

Your post is kind of spoilerish, but anyway this quest is quite buggy if you don't do it the way the writers expected you to do it. If not on PC you will probably have to go back to an earlier save (this is why I keep literally about a hundred saves going back several days). Otherwise you could maybe try committing a crime and then paying off your bounty. http://www.uesp.net/wiki/Skyrim:The_Forsworn_Conspiracy

PS there is supposedly a patch with quest fixes coming out in the next couple of weeks, whether they will get all of them is anyone's guess.

All I can say is that I found Marcath a nightmare for similar reasons. I'm not as bright as many here, and killed almost the entire guard squadron in that city before I decided that would make life too difficult elsewhere and I went back to an earlier save.

I would have liked a comeuppance in the plot line to handle the guards.

On console, go to an earlier save or restart or keep killing guards and hope a patch fixes it.
On PC press ~ click on guard type paycrimegold press enter. Do the same when it happens again. Hope a patch fixes it.

known bug
we hate it

This.

... and

~ spoilers ~

I encountered the same problem and (after not wanting to kill all the guards in town but doing it anyway) reverted to a prior save and completed the quest using another choice.

Thank you all for the information and help you have given me. I think I will continue killing guards until I see if the patch they are doing is going to fix this bug.

I went quietly to jail when I did that quest; would love it for my next playthrough if I can avoid that..

I don't think it would retrospectively fix the bug for your character if they patched it, I had it to and killed every killable NPC in Markarth - it's very quiet now.