The news coverage on Kojima has been iffy at best, so it's hard to be certain if he's legitimately left Konami. He's left, he hasn't, he's "on vacation," he's kidnapping baby birds or something, I don't know. It's getting ridiculous.
If you must know, our title choice is derived from a 1960s song called "Secret Agent Man" (I try to make references with the working assumption that the majority of our readers were born in the 1950s).
Anyway, regardless of Kojima's current employment status, I just hope he eventually leaves that terrible company so he can restart the Silent Hills project. But, knowing Konami, they'll probably cling on to that franchise to spew out more Silent Hill-themed pachinko machines.
One can only hope he gets snapped up by some other studio, or he just goes into the full on crowdfunded-indie dev route.