I realized this in a conversation in brightly_lit's comments (see http://brightly-lit.livejournal.com/20549.html ) ... in many ways, Dean treats Sam the way you'd treat a small child, especially when it comes to this issue of consent. Not just a small child, but a seriously ill small child. In 9.01, Dean treats Sam the way you'd treat your four year old who needs a kidney transplant. You don't ask the kid if he wants to live. You don't consider the moral implications of putting "someone else" inside his body. You just get in there and do what needs to be done. Because (a) keeping this kid alive is your most important job, the responsibility that trumps all others, and (b) even if it wasn't your job, you love him so much that you're going to do whatever it takes to keep him alive, even if it forces you to do something you know he wouldn't really want (and of course you convince yourself that it doesn't matter if he doesn't want it, because it's for his own good and he's really in no position to make that decision and the ends justify the means and good Lord, I could go on forever with this one, because it just doesn't matter, you can always justify saving the one person who you cannot let die). You know, and Dean knows, that it might make the child unhappy. And you want him to be happy, you really do, but if it's a choice between happy or alive, you pick alive. Every time.
Now, honestly, for Dean? I think it's more (a) than (b). Yes, he loves Sam, more than enough to want to keep him alive. But the times Dean really falls apart are when Sam dies because Dean failed him somehow (in Dean's mind, anyway). In season 2, he's taken right under Dean's nose, and Dean literally finds him a minute too late to save his life. In season 8, he undergoes the trials because Dean failed to kill the hellhound. And those are the circumstances that lead Dean to do really bad things in order to keep Sam alive. On the other hand, in season 5, not only is Sam dead, but he's condemned to eternity in the cage with Lucifer, and yet Dean carries on. Because it was Sam's choice, and it wasn't precipitated by a failure on Dean's part (unless you count breaking the first seal, which Dean and the writers do not).
Fans and fanfic writers like to presume that Dean can't live without Sam, but he's actually shown us multiple times that he's perfectly able (and sometimes even willing) to do so. In season 1, after initially balking, he comes to peace with Sam's decision to strike out on his own and is actually proud of him. In season 5, he's willing to separate from Sam even when he knows Lucifer is circling his baby brother like a vulture (and only takes him back when he finds out they make really bad decisions when they're not together). And of course in season 6, having accepted Sam's decision to sacrifice himself, Dean is very functional. Probably unhappy much of the time, but functioning. So Dean can live without Sam. He just can't let him down.
I think this is largely due to the fact that Dean was thrust into the role of parent/protector when he was four years old and John never took that role back. Keeping Sam alive became tied into his role as a brother. And you don't really outgrow your sibling roles the way you outgrow your parent/young child roles, so Dean never had an opportunity to step back and say "my work is done." Sam would have stopped being John's young child, but he never stops being Dean's brother, and for Dean "brother" will always mean "my responsibility."
So after a lot of rambling, I think my take on the consent issue is that Dean doesn't consider it an issue. When it comes to what he sees as his responsibility toward Sam, he's a very "ends justify the means" thinker. Whether Sam agrees, of course, is going to be another story.