This seems pretty unlikely.
Konami was incredibly happy with the response to P.T. There were internal talks about making P.T. its own thing, separate from Silent Hill.
Whatever happened with this game and Silent Hills probably has little to nothing to do with Konami Ebezeering over P.T. while Kojima is the trodden-upon Tiny Tim. It was probably simply that they no longer had a director for it, Silent Hill isn't exactly a hot property that can just go to any team because that strategy produced major bombs in the past, and their continued path into leaving retail game development.
I keep mentioning it and it keeps being ignored, but Konami had a number of major producer departures in the last few months. The producers behind Love Plus, which was a money-maker for Konami, left really abruptly about a week before this Kojima stuff broke. They're almost certainly restructuring out of games, so any conspiracy theory of what's happening here that is solely about Kojima and Konami is likely way off base.