[IXRollOutIX]

Well first, we don't know the entirety of Hiro and Masamune's conversations. Second, even without that information, I think it's still logical to assume Brave's state of mind regardless. Cronus is just too damn powerful. He can too easily completely erase Saki's data if Hiro even so much as attempts to double cross him. The "big picture" doesn't matter, because Masamune's threats are immediate. Even if they get rid of his pause ability, he's still a strong opponent. He could easily escape and delete as much data as he wants. Even if they remove his ability to transform entirely, so far they can't pin anything on him as the CEO of GENM. The ministry of health is clearly unable to shut down the corporation for one reason or another, and now they can't apprehend him for the same crimes he was charged with years ago either. He gets away scott-free and is able to make Hiro suffer either way.

If Hiro wants to save his girlfriend above all else, he really has no other choices here.