I don't think the rewards are limited if there is a chance that Snakes appearance in Brawl could garnish up some hype from people that might not of been interested in his series to begin with. All every one talks about is how MGS4 is going to be THE game to have for the PS3s*, that it justifies blu-ray, and how it will sell more systems for that game alone (etc.). I don't think Kojima wants his epic title to flop because not enough people own a PS3. If there is even the smallest chance to make his game sell better, he'll do what it takes for it to do so.
At this point all sony really has at after this holiday they've seemingly given up is a small chance from a big game.
so what if he loves the Smash Bros. games? That's not reason enough to want his character in the game, he wants money in his pocket, money he can make by exposing Snake to as many people as possible before MGS4 hits. When all is said and done he should be the one doing Nintendo the favors, not the other way around.
Even if it doesn't sell well because of the small ps3 uses base, nintendo can still call up Kojima when Brawl sales surpass MGS4 and be like “Hey look, your game sold X amount on ps3 but look, Brawl sold XX amount over Melee and thats partly due to your character being in it. Its obvious you've got some fans on our side of the fence, maybe you should make something just for us and see just how well those fans want your creations.” Thats the business approach i expect to be taken.
*FF purposefuly left out of statement