When we already have people with god-level powers, you don't even have to be basic human to be incredibly out-gunned.
I do see your point. But I would hope that the information provided explained why they were an inherent threat to everyone, rather than a rival organisation with a grudge against their personal enemies. (Which could include "they'll see everyone in the mountain as having sided with their enemies and target all of us", if that's the case.) Otherwise it's pretty subjective to include them and looks to outsiders a little as though their main problem was just plain not getting here first. Like, if we'd had a solid group of Torchwood One agents right from the start, I can guarantee they'd be putting the Doctor on that list. But if they turned up now? Even if they completely hated him, they'd almost certainly just keep their mouths shut.