After reading "The Last of Us and Grading on the Gender Curve" by Carolyn Petit, I felt the need to justify why I disagree with most of what is she says. The topic of whether The Last of Us is sexist or not is one I have seen raised only once (here) despite knowing a couple of women who have played this game. Firstly, judging by the section I've quoted below, I think that your view of the entire plot is skewed in the wrong direction. Joel is absolutely NOT a hero. That is the point in the game. In the Winter chapter there is an entire section where, playing as Ellie, you survive. She does not get saved by Joel; she kills David and survives by her self. She doesn't need Joel to survive and that is seen throughout the game. It's used so that the ending is even more powerful, Joel isn't the hero; he is a pragmatist and dooms the world for his own survival.
Reference: "But let's not kid ourselves about the nature of this relationship. Joel is the hero on a quest; like Frodo carrying the One Ring to Mount Doom, Joel must deliver Ellie to the Fireflies. Like the Ring to Frodo, Ellie sometimes gets Joel out of a jam. She also sometimes gets him into jams, and regularly slows him down--something you're reminded of each time you have to help her cross water."
Secondly, the end of the game avoids the obvious plot arc. Ellie does not die. And it's more powerful because of this. In other words... two plot-important women die in the whole game and they're right at the start. One is your daughter, so it isn't just because she is a girl that it affects Joel; it's because she's his child. The next, Tess, is probably the strongest character in the game. Why doesn't the game follow her? Because it would be terrible! The whole attraction to The Last of Us is that it allows us to play as a character who is broken and wrong and selfish. Tess wasn't that. In many ways Tess was more similar to the conventional game character than Joel. Just because she has breasts doesn't automatically make her a more ground breaking or less sexist character to play as.
I disagree with practically every point Carolyn Petit made in her article and I think I've given enough fair reasoning as to why. Gaming is an incredibly sexist hobby, and it sucks (as a gamer) to be thrown in with that stereotype - just look at the comments on the article about XBOX's new boss. There's plenty of valid points to make about sexism in gaming, but I don't think The Last of Us is one of them.