Even if he's still under employment there, why deny him the rights to travel? That shit even allowed?
Whatever is going on, it's some crazy contract that unfortunately seems Kojima signed and is now legally bound to. That probably includes not making public appearances on behalf of his games without Konami's approval. Just being there in the audience when MGS V is announced as the winner could be construed as a public appearance in support of the game. Yes, it's crazy that they are rubbing his name from pretty much everything he's done, but it seems to be the contract he signed.
It's also apparent that although Konami isn't interested in console development anymore, they certainly want to avoid Kojima from making console games for a competitor, or to create an MGS clone or new action-adventure franchise to directly compete and devalue what Konami has with MGS.
Lastly, although as a fan it's good that Geoff called out Konami for their business practices, we certainly don't want to make it any harder for Kojima. Konami could probably tighten the screws even more. Their actions of late seem to indicate they have no appetite to lose face and concede whatever war they are waging on him.