Yes, I think the idea of retconning Captain America as a Hydra agent is high on the list of stupidest ideas comic book people have had. But I'm not upset, because it's just a stupid comic book, and a smart writer will easily retcon it. If I was in charge, it would be explained as a bad dream that a Marvel editor had.
Captain America being a Hydra agent makes as much sense as:
1. Kal-El blew up