Kind of misleading what you originally wrote.
From the link:
So yes, originally Kitamura stayed true to the original. And yes, Kojima rejected it. But Kojima didn't tell him to make it more over the top, he just wanted Kitamura to do it the way that he (Kitamura) wanted to. It just so happened that Kitamura likes things to be over the top. I've only seen one of Kitamura's works (Versus), and I haven't played Twin Snakes, so I can't comment on whether or not it follows his style, but from the interview, all the cheesy cutscenes were the work of Kitamura.
OP: My favorite MGS game is MGS3. The only real complaint I have about the game is that while the boss fights were great, the bosses themselves weren't all that interesting.
Kitamura's known for high action films with similarly over the top spectacle, reread exactly what Kojima says "This isn't it. If we're going to have Mr. Kitamura do it, we want him to do it his way.". Kitamura's inclination was to stay true to the original games (likely due to being a huge fan of the game), while Kojima explicitly hired him due to the style of his films. Basically Kojima's saying he wanted the movies in Kitamura's film style (ie: over the top) or they wouldn't have hired him.
Besides which, the buck stops at Kojima. The cheese wouldn't have made it through unless he signed off...