I just found this out today when discussing Skyrim with a friend of mine. He told me that one of the final parts of the Main quest involves a council between just about everyone in Skyrim. Ulfric, General Tullius, and all the other heads of state are there to discuss Alduin. There's just one problem

I already completed the Civil War on the Stormcloak side, and Ulfric rather killed the good General. So... what the heck is going to happen now?

So now you will do the main quest as usual, minus the peace treaty. No big deal, in fact it means you avoid all the bugs.

Oh, really? That's good.

Not always true, the peace negotiations can sort out Markarth if you have done the prison break and can no longer go back there thanks to the gaurds.

The peace treaty is kind of a waste of time. It's not really a treaty, it's just a temporary cease fire so the dragon crisis can be addressed. So you didn't ruin anything by completing the civil war quest line first.

I never really liked the "peace treaty" because if feels more like the surrender of one side vs a temporary cease fire.