This is beyond unfortunate. Like Capcom, seeing that Konami logo will be like seeing a ghost of the past from here on out.
As for Kojima, I actually see plenty of silver lining here. For one, it's very rare that we get to see a successful video game series have a definitive, consciously planned ending. I absolutely adore Metal Gear, but I'm actually excited by the prospect of saying "this is it -- that's all there is." The story will end, and you can put them on your shelf like an old (absurd, bizarre, ostentatious) series of novels. I have no interest in Metal Gear without Kojima. It may as well not exist.
I'm also excited to see Kojima thrive outside of Metal Gear. One of the tragedies of this industry is that successful creators get tied to mega-franchises for years on end, something that has worsened with huge production budgets creating the "need" for insanely high returns. I can't wait to see Kojima's work after Snake is put to rest. After all, this man has had a hand in Policenauts, Zone on the Enders and Boktai, among others -- I'm quite ready for more.