It's up to the player, whether they want to have their own personal moral debate about what they're doing. You're forced into the path that Joel has 'chosen', and ultimately can't deviate from it. If you feel strong enough about Joel mowing down the Fireflies to save Ellie not being morally justifiable... I guess you'd just stop playing the game.
I for one took the game to completion without much compunction about it, but after the final scene definitely thought long about how ####ty Joel left things, having killed everybody and lied to Ellie.