Why should Ulfric continue to obey the Empire when his home land is being threaten by the Thalmor? It's all thanks to the very Empire that he fought for. The Empire gave the Thalmor permission to hunt down Talos worshipers.
"I fight for the men I've held in my arms, dying on foreign soil. I fight for their wives and children, who's names I heard whispered in their last breaths. I fight for we few who did come home, only to find our country full of strangers wearing familiar faces. I fight for my people impoverished to pay the debts of an Empire too weak to rule them, yet brands them criminals for wanting to rule themselves! I fight so that all the fighting I've already done hasn't been for nothing. I fight... because I must." - Ulfric Stormcloak
If Marcus was in Ulfric's shoes I'm sure he would do the same for his people.
Marcus never willingly gave information to the Thalmor, being their puppet. He may be unwilling now, but before he did the Markarth Incident, he cooperated with them fully. 'After the war, contact was established and he has proven his worth as an asset.'
People weren't hunted to extremes until the Civil War. Everyone still worshiped Talos, they didn't care about the treaty. Twenty six years to bitch about something, I don't buy into that crap. All this is, is just a coup d'etat for Ulfric's selfish ambitions, he never cared about his people, he wanted bloodshed. Yes, Skyrim has every right to be independent, but not like this. Not when there were peaceful ways.
Marcus isn't a war pig looking for glory and stories. If Marcus was in the same situation, he would of gone for the peaceful alternative. Without slaughtering his countrymen, nor would he accept racial segregation. I'm all for an independent Skyrim, just not the Stormcloak way.