So in actuality it's not that the only way to disinfect something is to do a clean install, in your opinion, but the only way to know for sure that you got it is to wipe the hard drive and start over.

Which, incidentally, is entirely different from reinstalling.

And no, magic is not involved. But there are nasty little things that like to do tricks like hopping from partition to partition, or simply hiding in the boot sector if you're not doing a high level format.