Make sure facts are straight. As said, the founders, the Stamper brothers, stayed long after the MS buyout. More importantly, the rumors and discussion internally for Rare to be sold started in 2000, and if anyone has ever worked in a company that is looking into changing ownership, that alone will spur people to look for other places to work that may have more stability and can lead to less productivity and some of the "turmoil" you might have seen leading up to the sale to Microsoft.
I think the blame ultimately has to rest on Rare and it's games, but Microsoft could have done more to push the licenses Rare had early on instead of ports and originals. Even if the originals were good, a brand new Conker, Banjo, or Perfect Dark during those later years of the original XBOX could have helped keep the Rare brand front and center in gamers minds. Instead the first Xbox Rare release was Grabbed by the Ghoulies....