The uproar wasn’t so much over the sound itself (which hasn’t yet been finalized, although guitarist Robert Fripp is apparently working on it). Instead, the concern was that Windows would not allow an easy way to change or disable this startup sound. At the time, the “controversy” seemed somewhat overblown, as Microsoft had officially stated that they had not yet decided whether or not to make the startup sound optional. Now, in a more recent (5728) build of Vista, the ability has now appeared to turn off the startup sound in the Control Panel.
It’s funny that something makes the news that shouldn’t even occur in the first place…