I'm guessing they're being extremely literal to make themselves look better than "the company that dumped kojima". I think it's exactly what you say - that he's using up his earned vacation time, but I suspect he doesn't exactly have an option to return to work after it's used up.

After all, a company doesn't go through great pains to remove all reference to an employee (kojima) from the works he's involved with simply because he's on vacation, if you see what I'm getting at there.