In what possible way could Sony have stopped Nintendo and Capcom (a 3rd party developer) from communicating to each other? This is a serious question because I have no idea.
With hindsight being 20/20, the obvious answer was to get Capcom to agree to an exclusivity deal when MH2P/F was turning out to be a genuine system seller. How do you not even try to cover for something like that? Nintendo wasn't going to be on DS-level hardware forever.