What about Ninja Gaiden 3's Wii U version? It was apparently being published by Nintendo but is now on PS360.
I think Nintendo distributed, but was published by Tecmo-Koei.
Being a publisher of an XBLA game doesn't involve splashing millions of dollars publishing it, in fact Giantbomb stated that publishing could mean as weak as just giving out slots (Like D3 always does) Those games were contracted on the basis of them being timed exclusive regardless of the publisher. Also, the fact you are comparing XBLA games to full blown AAA game is laughable.Most of the XBLA games like Limbo, Castle Crashers and Braid were published by Microsoft on the 360. Regardless of their timed exclusivity, Microsoft was the publisher of those games.
Regarding Mass Effect and Ninja Gaiden 2, it's not important how they changed platforms. The fact of the matter is that EA and Tecmo wanted them to be on PS3, so they found a way to make them on PS3.
That's the risk you run when you publish a game without owning the IP. As long as Microsoft doesn't directly develop the game in-house, there's not that much they can do if the IP holder wants to go elsewhere once the contractual period has expired.
As said, ME comparisons needs to stop. EA bought them and was allowed to do whatever they want with IP. I can't see anyone buying Insomniac, especially as they have stayed so long to be independent developer. And Ninja Gaiden games were quite an upgrade. One could say they were made so it would barely escape the legality of things. I thin Msoft by now would rather sign a full punctuated deal to retain any advantage from the competitor.
They can't do much once the contract deal expires but they have a choice of lengthening that time of the deal. Once that time arrives you would have moved on (Like Limbo)