Why are the Stormcloaks pissed at me now?

You may have a bounty in that region. Talk to a normal guard from the hold and see if you have to pay off a bounty.

Any one will attack you if your bounty is high enough

Not sure about that one. If you need to talk to someone though, you can use Calm on them & then try to talk.

It has nothing to do with Malkreath, it is a glitch in the game for all platforms at the moment. And here is an explanations of why you may be attacked out of nowhere from any faction or group... Factions are handled dynamically in Skyrim. You can go from being loved to hated just like that, but this sounds more like a bug. If they initiate combat with you, perhaps you can yield? Try talking to Ulfric Stormcloak also, maybe there's a dialogue option you can go through to make them friendly again. Nonetheless, the forsworn are a rival faction in-game, and aiding them makes your disposition fall with all opposing factions, thus why they became hostile.

Maybe try to reload you game before you enter the city and see if that helps if not try to contact skyrim on their forum. I hope this helps you understand a bit more if it does please help me out and vote my answer as your best, thanks buddy!!!!

shouldnt have done malkreath.