You sound confident in your narrative of the internal conflict inside Konami, treating is as established fact and not speculation. But, everything I have read about the internal conflict has not had the internal narrative of the individual players. (For example, this comprehensive piece at Polygon does not mention what steps Kojima took internally: http://www.polygon.com/2015/12/16/10220356/hideo-kojima-kona.... It does not have a narrative from inside Konami about who got fed-up with who, who initiated what, and how the power struggles played out.)

What have you read which gives more insight into what happened inside Konami? I think it's reasonable to assume that the changing direction of the company lead to the rift, but based on what I know, I cannot conclude that Kojima initiated his departure.