Joel is an...well...my initial response to his actions was that he's kind of an asshole, and while that may be the case, the fact of the matter is that he acted out of passion. It's kind of apparent that nobody discussed with Ellie whether or not she'd accept the operation, and there was no assurance it would even work. I can debate back and forth whether or not Joel was 'right' for what he did, but the fact that Ellie was left without a choice in the matter either way annoys me and makes me side with Joel just a little more.
I am pretty sure Ellis did agree.
If I remember right, the chain of events was Tunnel > firefly base > escape and in that time we don't see anything concering Ellie outside of what Joel learns. It's possible that the Fireflies lies to her about the severity of the situation or maybe she did agree, knowing that her life would maybe end the epidemic. Hmmm....I guess that does make sense, considering how much doubt she showed in responding to Joel at the end...
