Short term, I'm sure things will be fine (from here to the next 5 years or so). But it's pretty much always inevitable that as time goes by, people who made the decision to buy the company, forget exactly why, or are replaced by others who don't know, and only want to reduce costs. And so the company either ends up getting disbanded or folded back into the company and rebranded, with the ranks purged of long time (and expensive) employees, in favor of new cheaper ones that don't complain.
Look at Maxis. Even though the Sims is probably the biggest selling computer game ever, in order to cut costs, the most recent EP was done by a bunch of interns and new employees (who apparently bungled things very badly). I do think they let Will Wright do anything he wants, but even then, there are rumors that Spore has been delayed because the suits at EA don't think it's "fun" enough. (Never mind the same people said that about the Sims)
It's almost too bad that MS didn't buy them out instead. Would be no functional difference, really, and they seem to allow greater independance. But MS seems to be going out of that sort of business (letting Bungie go, disbanding FASA) and the shuffling of execs between MS and EA makes me wonder if they feel they don't need to, anymore, since they are working closer to EA these days (EA hasn't dropped support of Sony platforms, but does seem to be scaling things back).
