Historically, telling Tony that he can’t do something serves not as the detriment that it’s supposed to be, but as encouragement and motivation to do the forbidden thing. Saying that someone else won’t let him pursue a course of action only serves to goad him into disobedience that much faster. It’s been a fact of his life since he was old enough to make decisions for himself, and it continues to be one now.

His respect and feelings for Bruce won’t let him be an ass about disagreeing with him, but his mind’s already been made up. He’s made a promise to the Hulk. His faults notwithstanding, Tony doesn’t go back on a promise if he can help it, and he can help it here. One way or another, he's going to do this.

“How about I make you a deal?” Ordinarily, he isn’t the sort to compromise, but for Bruce, he thinks he can make an exception. “If something happens, you suddenly discover that you’re not as immortal as you claimed to be on the helicarrier or you reintegrate with the Hulk, I’ll reverse the serum. I can do that. It doesn’t have to be a permanent change. Doing a system restore to factory settings will always be an option.”