Kojima's a big boy and also a public figure who has to think about what he does and says. I don't endorse Konami's over-the-top behavior but I don't view everything from "Poor little Kojima" perspective either. It's not like Konami has a super-popular public PR person who can refute Kojima's claims without looking like a corporate tool*.
I'm going to play it from the other side:
I have an employee, he never stays on budget, he causes trouble with other employees, and badmouths my decisions. I finally decide enough is enough, and fire him. Then, he starts using his industry celebrity to publicly take jabs at my organization and it's products. As that executive, I'm not thinking, "Oh what a nice guy, amazing developer, much empowered, yes, yes." I'm thinking, "F*** this guy, even after I got rid of him he's causing trouble."
Of course I'm exaggerating Kojima's sins for the sake of effect...but then again, what do any of us know about how Kojima conducted himself day to day? He might be worse than I just said. Konami could handle this much better, too but if I was a public figure like Kojima, I would avoid commenting on my former employer in public forums, even in North America where the employer / employee relationship is WAY more casual than Japan.
I also think this should encourage game publishers to reconsider the "game god developer" approach to promoting their products.
*edited