So, it would seem Burke is adamant in her claim Kojima was fired by Konami execs, but this morning a response from Konami came in to Videogamer.com
Via Videogamer.com:
A Konami representative has denied Burke's claims, telling VideoGamer.com that the suggestion Kojima has been fired is "categorically incorrect".
With no easy answers out there at the moment, it looks like this whole debacle will continue to be shrouded in mystery. Just like an episode of the X-Files.