When the first credits started to roll, I felt unsatisfied from the end, simply because nothing totally unexpected had happened until that point. Ironically, I felt the EXACT same thing when Naked Snake was banging Eva in MGS3, only to be blown away minutes later.
The scene with Big Boss serves as
a) the big plot twist of the game and of everything that had happened until this point,
b) further explaining the motives of the Patriots and the people who founded the organisation,
c) the death of Zero -the man who started it all- and
d) the final peacemaking between the two protagonists of the series, Big Boss and Snake, father and son, and between Big Boss and his dead mentor, the Boss; giving each
character the peace he deserves.
If the game ended with the cliche "happy end when the main hero dies" would be a massive dissappointment for me. This is the easiest way to evoke emotion but it has been used so many times in films and anime nowadays that I've grown to dislike it. The way Kojima ended the game, Snake finally escapes from being a prisoner of fate (both from the Patriots and the Foxdie), receives recognition from his father and achieves peace until he dies.
Essentially, the final scene not only does not downgrade everything that happened in the MGS series, but on the contrary serves as the catharsis of the story.