Cap might end up being a Hydra agent in the MCU, but acting as a triple spy: as in, he is an ordinary american boy recluted for the supersoldier program but in reality he was recruited by Hydra before but in reality reality he was an american agent all along pretending to be a boy pretending to be recruited by Hydra.
I'll bet in the comics he ends up the same lol
That or he is truly a Hydra agent and then he changes his ways. Both solutions are equally boring to me, Cap doesn't need these twists to make the character interesting imo.