Personally, I wouldn't trust them to not break things myself. I know they may not be "amateurs" at low level things like they do to make this happen, but I still wouldn't trust it. This is why my suggestion would be to use some kind of disk/filesystem encryption. TrueCrypt should be able to defeat them putting it back on and allow you to restore (from a clean copy) the original files and get your CHKDSK back.
On another note, I don't think I'd have ever noticed this myself, every laptop I've had I end up installing Linux on because of all the crapware that gets included with the OS in the first place.
Wait, just by providing the SN of a device you can get them to modify the BIOS? (assuming that is how they would get rid of this BIOS-executed payload)
I wonder what else you can social engineer out of them with just SN. . .
How would you react if you find the builder of your home has installed hidden cameras in every single room? If you somehow find about it and call him he'll turn them off. No big deal, right? If you're a proper person you have nothing to hide anyway ...
So, aside from not being informed about it, this isn't a big deal.