Companies tend to be very protective of IP's that they own(or not) and go to lengthy extremes to make sure no one else makes money that they feel is rightfully theirs(even if it isn't). Many times these fights border on the ridiculous(see Avatar vs. Avatar: The Last Airbender).
When Brawl was released, allowing Snake to br included was a win-win. Nintendo got the money of MGS fans and Sony got to advertise Solid Snake to an entire new demographic, which would boost the sales of MGS4.
Now that Snake is in that Sony Smash game, there is direct competition. Anyone who would play Sony Allstars only for Snake could easily just pick up Smash4 and not even bother with the other. That possibility of losing out on potential revenue could easily be enough to keep Snake from returning. But you have the added factor of the next MGS starring Raiden and not Snake, so the advertising potential is greatly diminished.
Then again, I'm not a lawyer and I could be wrong. Kojima and Sakurai ARE friends(although I don't know how much that matters), and Sony could decide to not be a bunch of ****s, but I'm starting to worry about Snake's chances.