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Kerotan said:

He said he doesn't agree with the out come of the game although some of it could fit his timeline. 

It's not proper canon and not made by him.  As I said it fits in with acid and this new game.  Spin offs of the main series.  

He didn't agree with the approach to videogame design when making the game, but he had complete control over the story and cutscenes, as part of his collaborative effort with Platinum Games to finally make the game, and he was completely satisfied with it. The game wouldn't have been made had Kojima nor Platinum Games been involved, as it was noted by Kojima himself and Platinum Games' president (back then at least), Minami.

Kojima loved it, Kojima wanted to make a sequel, Konami had MGR fit into the timeline of their games and Revengeance Raiden makes an appearance in both Ground Zeroes and Phantom Pain, both Kojima-directed games. There's simply no reason to consider Rising non-canon, especially how it doesn't break or retcons anything from the games before it, aside from Raiden's personal philosophy at the end of MGS4.