Oh yes. He'd try, he'd maybe even hold out at first, but I cannot imagine that lasting for very long. Because you're absolutely right; it would be so much worse to go through it while he was in his right mind. And Hydra's always known just the right ways to break him. It wouldn't take too long before he was sobbing in between the play-by-play commentary they'd force him to continue with as they fucked him.

Don't be shy, anon, you're among friends here. We all want Bucky crying. He suffers so prettily.