Actually, it *is* a big deal. Reaching into my computer and changing files -- any files -- when I have expressly denied permission is wrong. Even with the best of intentions, mistakes happen. Recall the WGA disaster of a month ago where Vista machines went dark because they couldn't phone home? All Microsoft's fault, no malicious intent, but the incident should be a wake up call.
How would you feel if one morning you discovered your Windows validation had been revoked, only due to a mistake? They have demonstrated they can stealth-modify files. Even more troubling, the article states there is no way to learn what was modified or why -- only the date & filename are available. No KB article. This is not transparent behavior, and one is compelled to wonder why? If it's a simple bug fix, then say so. The fact they go to some lengths to obsfucate the matter is more upsetting than the action itself.
I utilize a fully-paid MSDN platform subscription for all my Windows test machines. It's not difficult to imagine a block of serial numbers accidently deactivated, and the news sent down the wire to my little herd of test mules. Suddenly I cannot conduct business. What recourse then?
Or try out this far fetched, but still plausible scenario: MS licensing policy changes, and XP schedules itself to stop working on a particluar date, forcing a migration to Vista?
Until we learn more, there is nothing good to say about these activities or by extension the policies they enact.