Imperials, They aren't led by a racist bigot and only wish to preserve and protect their own people, the banning of the worship of Talos is very likely a temporary thing until the Legion can regain it's fighting strength and wage war against the Thalmor to regain lost honor and lands. The empire has never simply given up so easily. The empire is hardly a puppet state, if given the chance to recover they would stand a chance at detating the Thalmor, especially if the dragonborn (presumably off camera) decides to side with them; skyrim and the lands of Cyrodill united stand a better chance of defeating the Thalmor rather than just the lands of Skyrim on its own. To me, the empire represents order, prosperity and security for the people of Skyrim if given time to recover. In the end I'd think security wise and economically speaking the people of skyrim would be better off versus some barbarian racist rebels with poor governing skills.
