I think you misunderstand the message of the game.
You arent killing gods in a sense, you kill false hopes made flesh. They are idols that those people summon, so that they solve their problems, instead of solving them themselves.
What the Warrior of Light does, is not killing their god, because they cant. What they kill is the urge to let deities work their lives out and reminding them, that their lifes are in THEIR hand and they should solve their problems by themselves.
Its not about believing in gods, its about wanting the easy way out, on general.
Endwalker deals with a different way of "easy way out",
Its not always the same.
At least thats what I think