I have to wonder if this power struggle between Kojima and Konami are in direct relation to MGS V's plot. If you think about it, there are so many odd undertones from the trailers that can give the impression.
First, Kojima was planning to exit back in 2008 with the conclusion of MGS 4, and it correlated with the graceful parting of Old Snake. But, now we've got a game (MGS V), where Big Boss is being hunted down by Zero. And now he's being called "Punished Snake", "Venom Snake". That said, I can certainly see how Kojima is being "punished", and how he'll have "venom" against the company that took away what was dear to him (e.g. stripping his name from advertisements, and renaming KojiPro to Konami Los Angeles Studio). Sort of like how Zero tried to erase Big Boss. Coincidence?