I think the "why I now think Tor is the devil" question is answered in the opening—because it has illegal/immoral stuff on it. I'm not sure why anyone would be surprised about this though...
EDIT: In fact, I don't think that the security scanner was even that effective: "around 5-10% of the registered users chose to run the scanner" (later, he changes this to 4-7%) and that "some of the users who opted to run the software appeared to be government or private researchers". I don't know what percentage of people using Tor for illegal activity would be incautious enough to run some random program on their computer, but I would be surprised if it was very high.