I'm assuming part of this has to do with Kojima actually wanting to finally end the Metal Gear series and obviously that won't sit well with Konami. Understandably it's the company's biggest cash cow, there's no way they'd let it go. They've likely taken over complete control of the IP.
This was bound to happen eventually. Hideo can't work on the series until his death.
Kojima: Alright, guys, I really think I'm done. I've "closed the loop", and I think I've taken the franchise as far as it can go.
Konami: So this is you're last?
Kojima: Yeah.
Konami: You're sure?
Kojima: Yep, I'm ready to work on other IP.
Konami: Heh.
Kojima: ?
Konami: You see, that won't be necessary.
Kojima: !
Konami: We appreciate your services, Mr. Kojima. They have been required ... until now.
Kojima: You...! You were never going to let me work on other IP!
Konami: Hah, you finally realized. We've given you tastes, here and there, but just to keep you happy making Metal Gear. But we're taking control now. You're fired, Shinkawa-san has been most useful in your demise.
Kojima: Shinkawa ... you betrayed me?
Shinkawa: ...
Konami: He's been there all along. Some might say he knows the franchise better than you.
Kojima: I won't let you take Metal Gear from me. I'll let it die before that happens!
Konami: Security, escort this man.
Kojima: I'll be back, just you wait ...
Konami: So, Shinkawa-san, what's next for Metal Gear?
Shinkawa: ...
Konami: Perfect.