It's been pointed out elsewhere but Kojima retaining the right to his own name (or at least the 'Kojima Productions' name) may have been his choice. He may have reached an agreement with Konami to be able to use 'Kojima Production' at his next venture, a consequence of this is the removal of his and his production company's name from future Konami products, not out of spite but in accordance with their agreement. Obviously this is just speculation on mine and others parts, but at does present a situation that doesn't require you to assume malice on Konami's part.
I just feel like if I was in that position even if my name on the box meant nothing, even if I didn't get anything for it being there I would still want it there. Kojima is MGS, and more importantly he played a huge role in Phantom Pain. If the agreement is true it still kinda sucks that they wouldn't even let him leave his name on his last project with him even if it was just the name.