First rule: if you want to introduce more diverse characters into mainstream gaming, don’t do it at the expense of fan favourites. Because then fans will not only hate the character but more damaging is connecting the dots of hate and characters diversity together. Going forward any sequel with a diverse new character will be met with animosity not because of their identity but because their entrance means replacing one that people spent years investing in.
That’s the problem in a nutshell. Not homophobia or hating women.
But can you recall ever seeing the same kind of reaction when fan favorites are replaced by non "diverse" characters? For example, when Snake was replaced by Raiden people were upset, but it wasn't met with this kind of reaction. When Dante was replaced by Nero for half of Devil May Cry 4, the reaction was not all that extreme.
If it is solely about replacing older characters, we should expect the same general level of outrage whenever an old character is replaced. But, that's not what we see. I'm sure part of the reaction is because of displacing beloved characters, but that doesn't explain it all.
Not exactly comparable situations because the method of replacement differs, namely that the previous main characters die in The Last of Us Part II (Joel confirmed, Ellie unconfirmed). That means that those characters won't return in future games, so the replacement has something final to it instead of being a temporary state like in your examples.
But on the other hand, you are correct that there's more to it on top of the replacement. I mentioned it in a previous post of mine in this thread that the current controversy provides a platform for people who push their own political narrative. They don't account for the majority of people who complain right now, but they are going to be very vocal about it, so the whole issue grows into something really big.
One amplying factor in this is that the medium video games is basically the last bastion of entertainment that is largely free of political messaging - movies, TV and the internet in general are already infested by it - so this creates more paranoia, fear and hostility in response to Naughty Dog's story-driven decisions.