I suspect some kind of jealousy going on in Konami's management body. Kojima was the most talented and most known among all executives and probably the only person who had his own studio within Konami. I wouldnt be surprised if some saw this competitively and hence wanted to get rid of him. The long development time was probably the excuse. Except from MGS and PES every other big budget game in Konami were going downhill. Everyone else was not meeting sales goals. The immediate transition to mobile games and the removal of his name in every project he worked on tells me there was potentially some kind of incompetence of others to maintain Konami on a high profile and didnt like his success.
And I am still very pissed that an awesome "secret" event that was going to happen in my country got canceled because of his departure. I was going to see him in real life