These two situations are barely comparable. In one situation, you have Pedro Pascal's father figure character disappearing from the show completely, in the other his character would have had to share the screen time less with his surrogate CGI muppet child being the one removed, it would've been more akin to Ellie being the one dying. Regardless, The Last of Us Part 2's flaws don't spawn merely from Joel's absence alone, and more what accompanied that. The Mandalorian season 3 didn't benefit from negating a character's arc that had concluded.

Grogu served no purpose in season 3's narrative besides to take more attention away from Pedro Pascal's (and others by extension) character. It was a purely business minded and marketing strategy. If you cut Grogu from season 3 though and go into the story with fresh eyes and no attachment to the character, nothing of substance is lost. Joel's absence is felt and supposed to be, it having negative side effects to the viewer is irrelevant. You can remove all of Grogu's contributions to season 3 and his absence will not be felt. If the average popcorn viewer is bored because the charming comedic moment or two is missing and they don't have a cuddable stuffy to adore, too bad... That may effect the numbers, but it in no way would have made the story or narrative worse. Grogu's absence from season 3 could've only benefited the narrative by being felt, instead he's a non-character who simply ends up existing in a season that he is irrelevant for.