I don't think so. Political correctness does suck but if it's on an overall good product people don't mind. Its only when the entire product revolves around political correctness that consumers start to take caution. As long as the main plot line in TLOU2 is not how Ellie is being persecuted for being a lesbian then im willing to bet it's going to be overall good. A little pandering here or there wont be a big issue.
When they first revealed the game, they spent a huge amount of that reveal time on that aspect of the game, which leads me to think that a huge chunk of the game will probably revolve around that. I could be wrong, but why else would they focus so much on that in the reveal moment, otherwise?