Rare most definitely jumped ship, The stamper bros sold their share of the company before Nintendo did making 100s of millions of dollars. Nintendo had the minority stake in the company, they didn't want to have any stake in a company that was not going to do what they wanted so they divested their part of the company for 200+million. Its just spin that Rare was doing terrible and had to be dropped. There were rumors for months on whether or not they were leaving Nintendo or not. Rare is a shell of itself now, but there is only like a handful original people if any still with the company. Not even the Stampers are there. They are rich and retired(from Rare at least).
Silicon Knights is always in need of a pimpdaddy publisher, the only reason for leaving Nintendo according to them was artistic difference, which because Wii was underpowered and weird seems to be the reason given they were aware of it before it was announced. Had Wii been powerful, what reason would there to put Too Human on any other system or for that matter to turn an exclusive gamecube game into an exclusive xbox 360 game?