The dossier only says he was captured during the campaign for White Gold Tower. He probably fought to the end to protect the Imperial City and probably was badly injured to the point where he could be taken alive. Given his personality that very much possible. Of course we don't know for sure, but to use him getting captured because he help defend the Imperial city to argue against him is laughable.
The Legion can't beat the Stormcloaks without divine aid either and the funny fact is that says more about the legion than it does the Stormcloaks. The Empire's own professional, well armed, disciplined and versetile fighters cannot beat an army made up of Nord farmers, barmaids, drunkards and old vets

Nobody says that Ulfric is to take on the Dominion alone. Even the most suicidal Nord who yearns for a quick ticket to Sovngarde is smart enough to know that Skyrim needs allies.