Because we, as a civilized society, look down on things like human trafficking, organized crime, extortion and so on. These activities require the ability to transact large amounts of value in untraceable ways, and so to the best of their ability the government try to prevent that.
This isn't about stopping this guy from doing what he was doing, it was about making him follow the same rules that everyone else who does similar things follow, which is more about keeping records than anything else. If he doesn't want to follow the rules, then fine, he can stop doing the business. His call - but no one MADE him stop.
It's amazing to me to hear the constant screams about Wall St "criminals" who need to be regulated even more than they already are, but heaven forbid the bitcoin freedom fighters get caught up in some of that regulation! The hypocrisy is truly breathtaking.