jamyskis: It's possible that he has holiday leave that he's taking now before he leaves the company. Konami stated that "he's still an employee" which for accounting purposes can mean as much as he's still on their books. They didn't ask the board - they asked some secretary/bureaucrat, who probably wasn't really aware of what was going on.
In addition to this, I strongly believe it's a face-saving move on the part of Konami. Even though they've lost the people behind Castlevania and Silent Hill, it's Kojima who has the most public recognition with MGSV and MGS:GZ still fresh in the gaming public's minds, and his loss is likely the most publicly embarrassing one for them.
As anyone who's lived and worked in an Asian country with a strong historical Confucian influence will tell you, saving face is a very important factor in the working and corporate culture. So much so that upper management/execs will bring their company to the brink of ruin just to save face (i.e. Sega).