Not really. All of the Metal Gear Solid games have their little jokes. Ever call Rose or the Colonel (I forget which one triggers the scene) while standing under that soldier's urine stream in MGS 2?

MGS3 isn't the first game to have crazy supernatural bosses. Fortune could swerve bullets out of her way with luck. Vamp is basically immortal. Psycho Mantis could read people's minds. Vulcan Raven could control birds.

As for The Boss with her costume, it's not any more crazy than Solid Snake's sneaking suit.

Besides, the ending was heart wrenching. MGS3 SpoilersSnake kills the woman who is basically his mother figure and finds out that it was all a conspiracy and she hadn't really done anything to deserve it. She was a hero who would be remembered as a traitor forever. Nothing crazy and goofy about that.

EDIT: If you're sincerely unsure about whether or not MGS3 is canon, it is. MGS4 spoilers that have been revealed in previewsEva is in MGS4 and I'm pretty sure they discuss what happened to the philosopher's legacy.