Ian, there's a problem with your logic. The only games SK did with Ninty were ED and MGS. AFAIK, SK's major game history goes like this:
Blood Omen: Legacy of Cain (the original game of the series, whatever that was called)
Eternal Darkness
Metal Gear Solid: Twin Snakes
The first was a critical success, if not sales success. The second was a critical success, and largely developed for the N64, before SK went second party (though even SK admits a good deal of help from Nintendo). The third was, well, you probably know about the third better than I do.
The short of it: Nintendo helped SK, they didn't make SK. If SK goes third party, I'll still respect them, and more seriously question whether to purchase their games. If Microsoft buys them, they are dead to me. I used to really like Bungie and Rare, too. The moment M$ folded them in, they were dead to me, end of story.
Retro Studios, OTOH, is a completely different story. Nintendo literally made them, and I would honestly like to see Nintendo do something like that again (make a first party studio, that is). Then take two or three first party studios, and give them a different brand, to distinguish them as a "mature" (read: hip) brand.
I doubt it'll happen, but here's hoping.
BG