Capcom's official response to that seems to be...
"It was a knee-jerk response to a shareholder's request that we do something to make Capcom's stock value go up. It was an instant response, and we most likely lost sales on the title, because we're stupid morons, and the concept of 'timing' is unknown to us."
The other theory is basically the same, if you erase everything after "most likely lost sales on the title," and replace it with "because we have great love for PS2 owners, and wanted to let them make their own informed decisions about whether or not to buy a GameCube, without any of this talk about 'third party support' on the GameCube getting in the way."
There seems to be another reasonable theory/rumor going around. It says that the shareholders wanted the stock price to go up, so Capcom decided to go with their usual scapegoat, and slash some GameCube support. They decided to port RE4 to the PS2, but Mikami refused. Then RE4 went over it's budget, so Capcom cut RE4's funding entirely, and told Mikami that he could only finish making the game if he allowed the PS2 port. Mikami caved. Then Capcom went to Sony with the good news, but Sony doesn't allow ports unless the Sony version is declared "superior". RE4 pushes the GameCube, so it'll look like crap on the PS2. Even with "extra features", the PS2 version will still be the inferior one. Sony agreed to let it slide, just this once, but only if Capcom agreed to publically shaft Nintendo.
This was probably in the works for a long time, since Mikami announced that he was moving to Clover a long time ago, which is apparently his big response to this whole thing.
(Moving in protest from Capcom to... Capcom? You're a wuss Mikami. I'm not asking that you go 'all the way' and cut your head off, but this is just lame.)