Join Ulfric's side he is a much more creative leader than Elisif or Tullius, and he'll likely fight with the Imperials against the Stormcloaks anyway. AND he'll bring the thuum to bear against the Thalmor.
Well, consider:
1. Ulfric's rallying cry, religious freedom, is a just cause. On the other hand, it's a problem he caused. Until he made an issue of it, the Empire was happy to simply ignore the Talos-worship (indeed, many probably worshiped Talos themselves; Legate Rikke and Jarl Elysif being two examples). However, once Ulfric raised the stink he did, the Empire had to fall in line with the Thalmor in enforcing the ban.
2. Ulfric's character and motivations are cloudy at best. Some people insist that he is a hero and a visionary. Others have equal conviction that he is more interested in what's best for Ulfric than what's best for Skyrim. The information in "The Bear of Markarth" is especially troubling. Still, Ulfric may be more complex than either side gives him credit for.
3. The White-Gold Concordat is nothing more than an Altmeri plot to tear the Empire asunder and make it easier to conquer. It caused Hammerfell to break away, and the Altmeri lost no time in invading Hammerfell as soon as it was alone and vulnerable. Now, Skyrim is trying to break away, and if it does, then Cyrodiil and High Rock are seperated by an independant power hostile to both of them. Forced into an independant state that it didn't want and wasn't ready for, the Bretons will probably be an easy target. And if High Rock falls, it will serve as a jumping point into Skyrim, or a source of a two-front war for Hammerfell. In other words, supporting the Stormcloaks will more likely than not cause the Empire to fall, and the Aldmeri to overrun Tamriel. That is what the elves expected, and the reason why they banned the Talos-worship in the first place.
That is why, in my opinion, the Empire is the most logical choice.
1. Ulfric was thrown in jail for worshiping Talos after a Jarl agreed to allow free worship(which meant he hadn't been allowing it before) for him and his men.
2.The Bear of Markarth is written by an imperial writer who most likely heard about the Markarth incident from other people/reports. At best it could be considered biased and, at worst, propaganda.
3. The Aldmeri Dominion invaded and conquered Southern Hammerfell during the great war, and Cyrodiil signed over that land in the peace treaty. The warriors of Hammerfell pushed the Thalmor out of Hammerfell after the war and took back most land. If they hadn't left the Empire, that fight against the Thalmor would require the Imperials to side with the Thalmor and enforce the treaty or throw the treaty out the window.
High Rock wouldn't fight against the Nords...they have had a history of working together, and will more likely join them if the Empire tries to force them into a war with Skyrim.