The only major death in The Last of Us of a gay character was Riley, and that wasn't even in the base game. It's understandable that people are tired of gay people not getting happy endings, but the trope doesn't exist to mean that every case of a death of a gay person is "bury your gays".
Riley's death was written well before either of their sexualities was explored, it's part of the dramatic irony of Left Behind, unless you're going to argue that Left Behind wasn't well written, since you're insinuating that TLoU II probably won't be a well written game?
Death is a big motivation for people, and for Ellie it's one of her main character components. Riley, Tess, Sam, Henry, all people who died one way or another because of her simply being where she was on the journey. There are very egregious examples of bury your gays in media, Left Behind is not one of them and I wouldn't even say it's an example of bury your gays since the story doesn't focus on Riley's death, but it focuses on their relationship and it doesn't even show what happens to Riley. It wasn't using her death as a cheap shock moment, it was creating the full contextualization for Ellie's initial motivation that kept her going and kept haunting her after Joel pulled the plug on The Fireflies.
As for the trope that gays can't be happy? Ellie is a main character who is gay, even if she wasn't fully "happy" at the end of TLoU, she did find some type of peace through the lie that Joel offered ( at least my read on the situation). We see her five years later grown up, being relatively normal and so on. I'm not counting on Ellie getting a happy ending, simply because the path she is taking is a classic revenge story. And that's fine, having something be as classic as a basic revenge plot doesn't mean it's "unoriginal", plenty of movies, books, media in general recycles the same basic plots. Almost everything we write about has been covered by the Greeks in their stage plays, you can boil anything down into it's core dynamics and find that it's been hashed out before.
And this kinda goes into the main issue in this topic, is that Ellie is gay. That's not an issue obviously, but the issue is because she is gay and the logical outcome of that is her love interests will be... well, gay. It's why Left Behind is getting (wrongfully) pulled into this, because they wrote Ellie as gay in a tragedy. But just writing a gay character and having them in a tragedy doesn't complete the description or intention of the trope (as you said).
It's almost like people have flipped the odometer, to where the "non-problematic" way to have written Left Behind was have it be a close friend and not a gay love interest be the one to die... the same exact excuse people used to pretend Ellie wasn't super fucking gay or that "it was just a friendly kiss between friends!".
The trope is a trope because in media, gay characters who were relegated to side stories/B plots get whacked for the sake of shock value or it being their only defining characteristic. This is not what happens in Left Behind, I wouldn't even say it's what happens to Bill because his characterization is way more than his sexuality and his partner dying.
Vito from The Sopranos is a prime example of what the trope is. A character who was outed as gay and who is killed by his crew for being gay. Denise in Walking Dead getting offed to where the antagonist mocks the main character, saying "I was aiming for you actually", laughing at that missed shot while one of the only lesbian characters in the show got killed because he couldn't properly aim a crossbow. Steve Cortez from ME3, a character who's only actually characterization is that fact that he is gay and his husband died who basically spends the entire game in grief about that one singular event.
None of what happens in The Last of Us or Left Behind is close to the levels of what the trope represents in media. That doesn't mean it shouldn't be discussed in terms of the overall media bubble of how gays are written and treated in stories, but people are slapping on this trope like it's a perfect dress that fits everything it touches, when in reality they are ignoring the actual important stuff that defines the trope because of one basic definition fits the criteria in TLoU/Left Behind, dead gay people in stories.
The conversation has gotten pretty much out of hand and you're right in the fact it probably wasn't going to be a good discussion in the first place due to how the thread was created. When folks are writing about how Sarah dying is "problematic" because she's a daughter who dies at the start of the apocalypse (ignoring that Joel literally drives by a family with a kid five minutes into the game with the obvious implication they all die very fast and probably very brutally) tells me that people who are trying to argue some of these points aren't doing so in good faith.
Ellie is a fairly complex character, her sexuality is a part of that and it's important to not gloss over it. Now, I'm biased because I'm a sucker for tragedies and characters having horrific falls from grace, so Ellie turning into a monster and losing any semblance of humanity sounds like an amazing story to tell because of the parallels to Joel when he lost Sarah. The question then seems to be, if you have a gay lead, should you force yourself to restrict character motivations, inciting incidents or just stories because of being aware of tropes that have been harmful in the past? The answer is obviously no, but being informed about the tropes (which I think we should all assume Neil and Haley Gross (they are co-writing the game) fully understand the tropes they are potentially encountering) is important in terms of making sure you don't just fall into the harmful pitfalls that the tropes can easily fall into. Based on the history of Naughty Dog in general, it should be pretty safe to assume that the game is going to be well written to where they acknowledge and understand tropes in media during their writing process.
