Also, Square owes a great deal to Sony for bailing them out after The Spirit Within disaster... I suspect that's why they are still supporting Sony even though it has clearly lost market leadership.
Sony didn't bail them out... they bought a percentage of the company because they saw an opportunity to make a profit from the investment. Square, meanwhile, has kept its main series on Sony's consoles because it made good business sense -- because the PS2 was so dominant last gen, and most likely because they have a contract this gen. There's no such thing as loyalty among multinational corporations.
I don't know why people are talking about Square supporting Nintendo in a hypothetical way, anyhow. At this point Square is pretty much a completely neutral third party giving support to every platform on the market. The only further step they could take would be to share IPs, I guess, but I'm not sure what the advantage would be. They're both pretty competent developers who can manage their own franchises.