Wait a second, I thought this was in the spoilers section..

Oh it was moved. Not to stab my lower left part of the brain with a knife.

Well I didn't help them on their battle and didn't get that permanent bounty. Anyway I got problems with that quest. My Nord cannot worship Talos anymore in Markaths Temple because there are three corrupted guards waiting for him and giving him 1000g bounty for nothing every time he enters the shrine.

I did this quest with 4 different characters at various levels and different points along the main quest/civil war quests.

One character had done nothing with the main quest or civil war quests. Escaped the mine without siding with the forsworn, and stayed back. Still got attacked at the Talos shrine and stuck in and endless loop.
Another character completed both Civil war and main quests and did side with the stormcloaks. Got attacked at the temple with endless loop of dialogue and had to revert to earlier save.
One character sided with the forsworn and still got attacked.
One did only the civil war quests handed the city over to the stormcloaks and still got attacked on entering the city.

I really think it's a bug. I haven't played on the Imperial side yet.
I'm just avoiding the quest.

I know this happened to all of my characters. I really hope this is something Bethesda is working on.

If you do the jail break before the big Clan and Imperial meeting with the greybeards you can hand Markarth over to the nords during the negotiations it will allow you back into the city as the old regime will be in exile in Solitude.
I only found this out myself purely by chance, on the PC but I think it would work on consoles too as it was done without any cheats and only a mission based solution.