In my opinion, the Empire is the way to go. As many characters point out, the unification of Skyrim should be top priority, and that unification needs to be with the imperials for either faction to stand a chance against the Thalmor. To say that the imperials wanted to get rid of Talos is wrong, Tulius even allows Rikka to commend Gulmar’s soul to Sovengarde without causing an incident. As much as the nords, the legion is forced to forgo Talos worship, and it’s an even more pressing matter for them since they share a border with the Dominion.
Ulfric only leads the rebellion for his own goals, he doesn’t care about the people of Skyrim, all he sees is true nords and everyone else. He separates the populace, causes a social divide, and murders those who don’t bend to his will.
I believe Talos is a God, but the Stormcloaks alone can’t defend Man from Mer, only a unified Empire can.