Can anyone think of a single MS purchase where the employees did well out of the deal, leaving out the original owner?
Not just MS. I know people who were at small or very small firms that were either directly or indirectly acquired by very large firms (e.g., IBM, HP, General Dynamics, etc.). Not a single one of those friends or acquaintances remained with new large parent company past a year or two. In every instance they mentioned how at first things seemed fine, be eventually the parent wanted to fully assimilate the new acquisition, which meant a loss of the old company culture, structure, etc. Invariably, there were pay cuts, removal of perks, reorganizations, office closures, relocations, and all manner of other changes that would definitely challenge the morale of those who liked the environment of the smaller company.
As far as I can tell this seems to be a potential problem when any large and established company acquires a significantly smaller and/or less established company.