I sure hope Sony isn't making a mistake here.
After missing out on a few key projects and developers, like the game Remember Me, and From Software exclusivity, I expect them to be more bullish on letting creative folks do what they want.
Kojima is awesome, but if this goes poorly, I could easily see Sony not knowing when to step in and stop/guide him.
I think I used to think Kojima was the greatest game director, and therefore was infallible, but I think Konami wishes they hadn't thought that for so long.
Regardless, either way I get a (probably awesome) game. The difference is whether I get another one afterwards, and whether it takes 5 years for the first one.