The Fireflies and just about everyone else Joel had to kill really didn't do themselves any favors. I don't get the "Joel is evil" or "Joel isn't any better than the people he killed" that some of the review sites (IGN in particular) have said. Sure the game is a series of grey but there are a few clear things:
The people he killed were much worse on average than he was (at least in the game time). The only real deaths I could fault Joel on in the entire game was the Doctor and the end MAYBE Marlene after the elevator scene. Everyone else, and I mean everyone was pretty much a total piece of shit. Either looking to rape / eat them or just kill them for their shoes / cloths. I have no sympathy for him killing them because not only did they deserve to die but it was clearly a case of kill or be killed.
Joel can say that through the entire game, except the very end, he killed those that shot first. Those other fuckers had stacks of innocent people all lying around dead. Not even close in comparison. Now sure he mentions at one point that he was on both sides of the raids but I'm just talking about from what we see in game.
As for the hospital scene (last part) here is how I look at it. Fire flies did things in a really fucked up way. Take the kid for less than 24 hours, give her a MRI, prep for surgery and say oh well fuck her we're getting the shit out and we'll worry about what we can do with it later.
If they had taken a couple of weeks, did tests and slowly worked towards that I think Ellie would of had the opportunity to sacrifice herself as a last resort. Instead they strong armed basically her adopted father who went through hell saving her and tried to bully what they wanted out of them. In essence treated her just like a piece of meat, just like any of the other groups would of, all be in it a noble goal, but in the end just as uncivilized.
So Joel's reaction to them, IMO was more than normal. I mean if that happened to me and my daughter I'd probably go out swinging as well. The entire way it was handled was terrible. Joel was also right about one thing, Marlene would of kept on coming so him blowing her away was really the only way it could end for those two. Unfortunate because her goals were noble she just went about it so wrong. "fuck you, you're both here, kill the kid and we'll see what we can do with this shit we take out of her later".
As for his lie to Ellie. Well that will bite him in the ass on a sequel. Assuming there will be one. I see it like this though:
She'll grow to love the compound despite the issues there.
She'll fall in love
She'll lose her love around the time she finds out about the lie
They'll set out on a new mission (similar to what Joel did to Bill, "you owe me fucker")
In the end she'll either sacrifice herself or go to sacrifice herself but find out she is pregnant. Baby will have the antibodies and save the world
Joel's selfish action would still save the world and Ellie and maybe throw in something about how that particular doctor group Joel blew the fuck up at the end of the first game were just hacks and didn't have the right plan at all.
Happy ending.