The problem with Ground Zeroes and whether or not the ending is ignorable is that you can not, can not, can not convince someone who thinks Kojima is the greatest writer in the world that he fucked up. The ending of MGS4 won't convince those people, nothing will.
Kojima punches above his weight class, he manages to write some incredible things given the constraints of the medium, the language barrier, and other obstacles. But he has a lot of missteps that, because of his reputation, people are more than willing to write off as merely one piece of a large puzzle. He's not Xanatos.
No writer in the world is as consistently amazing as fans of Kojima think he is.