After completing the Markath quest involving the Forsworn and helping them escape I am still being flagged as a traitor and arrested/attacked on sight. I have already been pardoned but now I am a criminal again. This seemed to start back up after doing the Thieves Guild quest to obtain Calcemo's notes on Falmer.

You could try one of these from:
http://www.gamesas.com/index.php?/topic/1261066-complete-command-list/page__hl__complete+console

0x10C1,                      , 0, GetPCExpelled, , Faction0x10C2,                      , 0, SetPCExpelled, , Faction ~ Value0x10C3,                      , 0, GetPCFactionMurder, , Faction0x10C4,                      , 0, SetPCFactionMurder, , Faction ~ Value0x10C5,                      , 0, GetPCEnemyofFaction, , Faction0x10C6,                      , 0, SetPCEnemyofFaction, , Faction ~ Value0x10C7,                      , 0, GetPCFactionAttack, , Faction0x10C8,                      , 0, SetPCFactionAttack, , Faction ~ Value

I'm not sure if any of them work but its worth a shot.

Try one of these factions

[00] Skyrim.esm \ Faction \ 000A75BD  [00] Skyrim.esm \ Faction \ 0006566D  [00] Skyrim.esm \ Faction \ 000F9AB3  [00] Skyrim.esm \ Faction \ 000CD131  [00] Skyrim.esm \ Faction \ 000F17F1  [00] Skyrim.esm \ Faction \ 000656ED  [00] Skyrim.esm \ Faction \ 0009CA0A  [00] Skyrim.esm \ Faction \ 00065671  [00] Skyrim.esm \ Faction \ 000F18EA  [00] Skyrim.esm \ Faction \ 00065677  [00] Skyrim.esm \ Faction \ 000F122C  [00] Skyrim.esm \ Faction \ 00104646  [00] Skyrim.esm \ Faction \ 00104645  [00] Skyrim.esm \ Faction \ 000656EB  [00] Skyrim.esm \ Faction \ 0009DA2B  [00] Skyrim.esm \ Faction \ 000F18F0  [00] Skyrim.esm \ Faction \ 0009CA0B  [00] Skyrim.esm \ Faction \ 00065675  [00] Skyrim.esm \ Faction \ 000F17EB  [00] Skyrim.esm \ Faction \ 0006566F  [00] Skyrim.esm \ Faction \ 000F994E  [00] Skyrim.esm \ Faction \ 000F994D  [00] Skyrim.esm \ Faction \ 000F9965  [00] Skyrim.esm \ Faction \ 0004C446  [00] Skyrim.esm \ Faction \ 00104647  [00] Skyrim.esm \ Faction \ 000656EA  [00] Skyrim.esm \ Faction \ 000C78E5  [00] Skyrim.esm \ Faction \ 000D6733  [00] Skyrim.esm \ Faction \ 0006566B  [00] Skyrim.esm \ Faction \ 000656E7  [00] Skyrim.esm \ Faction \ 000656E6  [00] Skyrim.esm \ Faction \ 00094389  [00] Skyrim.esm \ Faction \ 00028178 

Yeah I'm not sure which could be it. I assume it's the guards, so that would be the whole town?

The way I solved it was:

1. Stashed all my stolen items.
2. Fast-traveled to Makarth.
3. Ran as fast as I could to the Temple of Talos and entered, yield to the guards inside if you can - if a guard follows you in, cast calm or something on him - you're looking to talk specifically to the guards that are already there.
4. Agreed to go to prison/pay my fine with the guard (can't remember if I had to pay any fine, but you don't need to go to jail - step 1 is just a precaution, I didn't have any stolen items at the time.)

After that, there was no issue. If you've killed the guards from that quest, I'm not sure how to solve it - maybe you can resurrect them with the console.

Yeah I made the mistake of refusing to go to prison when I first went back in and the whole thing kicked off The quest expects you to go to prison and find the solution in the mine. I loaded a previous save and all worked fine when I choose the prison option, but I was just doing the Forsworn quest I didn't have any stolen items on me.

The only reason that I discovered the fix was that I'd not been in Markarth since doing that quest (I slaughtered everybody, found the hatch and left) and got a good 5 hours questing and exploring done, then when I returned I noticed that all the guards were suddenly hostile to me. I spent a good hour messing in the console, massacring all the guards in the city only for more to appear and attempting to talk to the Jarl about it before I returned to the Temple. The problem was suddenly resolved!

Yeah I killed them. Will try inside and resurrect if dead.

Doesn't work for me. They still go hostile and murder me.

Try this. Open your console, click one of the guards and type paycrimegold . I don't know for certain if it works in Skyrim, though.

I have a similar problem in Markarth. Some time after completing the Cidhna Mine quest, I was in Markarth again on an unrelated quest. I decided to visit the shrine of Talos, but when I entered, I was attacked by two guards while another started the dialogue sequence from the Cidhna Mine quest. The body of the guy they had murdered was still lying in front of the shrine.

When doing that quest initially, I did kill two of the guards before I fled, and eventually surrendered. My stats show that I have a bounty of 2000, but no other guards in Markarth seem aware of it unless I enter the shrine of Talos. I can even engage them in conversation. But as soon as I set foot in Talos' shrine, all hell breaks loose.