That argument is a bit like the idea of colorblindness when it comes to discussing race, however. It doesn't do justice to be dismissive of identity in the name of equality because that ignores the different social contexts that are inherent to that identity.

I would say the fact that it is a gay love story is very significant to note for that particular episode given the time period that The Last of Us takes place in. What I mean is: society collapses in summer of 2003 in the Last of Us TV series (10 years earlier than the game). These characters are living in Massachusetts, which is one of the first states to recognize gay marriage, but would not have occurred until late 2003 if society hadn't collapsed almost overnight earlier that year. Obergefell v. Hodges would be another 12 years off, making widespread legitimacy of gay marriage a distant fantasy.

These two characters, effectively, had to live their entire lives closeted in a broadly homophobic society that would not recognize them. But it was after the collapse of that society that they were at liberty to be their true selves and, as we see, become happier after the apocalypse than they were before. It would not be the same story at all if it was turned into a hetero relationship.