You missed a key part of the story where the undercover agent told the bitcoin seller that he was going to use the bitcoins to purchase stolen credit card information. Thats the key part in this case, and probably the only reason an arrest was/could be made. It's one thing to exchange bitcoins for cash, it's another thing to do it when the buyer specifically tells you he intends to use the bitcoins for illegal reasons and you STILL go through with the trade.
"According to court documents, the agent told Michelhack that he wanted to use the Bitcoins to purchase stolen credit cards online. "
http://krebsonsecurity.com/2014/02/florida-targets-high-dollar-bitcoin-exchangers/Like I said earlier, it's a legal form of entrapment and it's something law enforcements do for all sorts of illegal things. The issue here isn't so much bitcoin , but selling bitcoin to someone who told you they would be used for a crime.
Your link has more details. Cops are still jerks, for entrapment. Luring people to commit crimes then arresting them is always going to be wrong in my book, but you are right that the issue is that cops are jerks ... but this is not an outright attack on the bitcoin itself.
Thank you for your link.