I think people should just side with who they feel is right, that's the point of the Civil War, there is no good or bad people in this, Though the Empire bribed most of the Jarl's when the ban of Talos happened, sent them chests of gold to not go against it, so Ulfric is fighting for the freedom to praise Talos, the Empire want's Skyrim to follow the Law's and ban Talos for the time being, which to many Nord's is how they put it "They may aswell of asked us to cut off our ear's" Nord's are very proud people, that value honour and tradition that is somewhat strange to the Empire, in Skyrim you can issue one on one combat with the King, if you went to the Emperor "I challenge you to a duel" and draw a sword, you'd have 300 arrows in you.
It's war, nothing is going to be perfectly good or evil, you do things as for the Markarth incident, you have one person's view, but the Empire said to Ulfric's Milita "You can worship Talos" they said they could, but then ended up arresting the lot of them. I prefer the Empire because it's how I view the civil war, but I don't try too much to think about it, the more you end up thinking about it, the more you end up hating both sides, many people's view's towards to Empire come from other Elder Scroll games, the strong empire you know, but you have to take 200 year's into account, the empire is a shadow of it's former self but who know's the Empire may come back or it may indeed crumble, no amount of saying "You should side with the Empire" or "Stormcloaks are better" will do much, people view war differently, people view sides differently.