"I think this rumor can be debunked using basic logic.
If Nintendo had a problem with Capcom, why do we have:
Zack and Wiki?
Every Phoenix Wright Game Ever?
Resident Evil 4 Wii Edition?
Resident Evil: Umbrella Chronicles?
Megaman ZX/ZX Advent?
Megaman Battle Network 8974952374 3D?
Capcom saying "we'll put Bionic Commando on the Wii if the fans show enough support?"
Harvey Birdman?
If you want my take on why Capcom wasn't involved with Brawl, it would have to be that Nintendo is saving Megaman for the next Smash game, since Sakurai likely won't be working on it, and Megaman would provide fans with an incredible amount of justification for the upgrade from an already-solid game.
According to the Iwata Asks interviews of Sakurai, Iwata had planned on remaking Melee for the Wii by throwing on a new coat of paint, refining the characters (likely adding a select few), and including the same basic type of online play that we're used to (random matches and friend code matches)."
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