This sucks. Kojima basically is Konami, without him they are likely going to really fall off. I hope this doesn't dramatically affect Silent Hills, but it's hard to see how it wouldn't.
The good news is this will hopefully give Kojima freedom from Metal Gear. As much as I adore the series, I want such a talented and creative guy as Kojima is to be able to make the game he is passionate about making instead of being talked into doing another Metal Gear Solid.
Also, no mainline Metal Gear Solid game should ever be made without him as a consultant. If MSGV is the last new MSGV game I ever play, I might can handle that. I don't want Konami forcing one on us and it turns out to be a big step down.
It's probably too early to speculate, but what's the likely landing spot for him if he does leave? Or will he start his own studio? Honestly, I'd like to see him go to Sony and maybe even head a new studio or even SCEJ (or high up there), because they seem to have a good relationship, they would give him a lot of creative freedom and they have studios he already has worked with (I think) like Sony Santa Monica plus the obvious movie potential with Sony Pictures.
Of course on the other hand I don't want to deprive other platforms of his games. I just want him to be able to make the games he wants.