I always thought Konami would never live without Kojima, he's literally the face of the company and they depend on him more than anything.
Now we'll see what happens, I don't expect them to continue as is at the very least. I don't expect them to shut down, but certainly they lost their ace. Of course it also depends if Kojima will work with them still or if he's out for good.
Kojima though, is safe no matter what he does. He's a legend industry-wide. He'll never be without work and will still make great stuff. He ain't got nothing to worry about.