Cult or crazy very likely. The whole "magic is not real" thing makes that designation very likely - plus many are probably a bit strange.
Terrorist or gang - not so likely. If magic is not real, they hardly seem dangerous. They are a mixture of people from all walks of society and tend to be led by old women (witches) or men (wizards) as these individuals have the most skill. Very few engage in illegal activities.
Consider how it would look to an outsider; mysterious deaths and/or kidnappings occur, and activity among these people increase. It seems like they speak in code to someone who isn't clued in. "We had another ghoul attack," for example; how would someone gathering intelligence interpret that? To some, things might look like a territorial or criminal interest dispute. Then they call in help from people like Dresden, who is definitely on several terror watchlists by this point...
While they don't have direct evidence of criminal wrongdoing against the organization, suspicion is likely super high. I could see a Mulder or two examining the Paranet as a massive enterprise. But, you know, with people like Tilly having some kind of understanding, I doubt we'd see some kind of crackdown from uncorrupted sources.