The ally thing is awkward, yes. It forces us to be more condescending to potential allies, such as the Bundschuh, Unioners, etc.
The ruthless attitude is necessary, but I can see us taking advantage of, or even aiding (perhaps for selfish reasons), other revolutionaries.
I'm not in favour of a full-on Terrorist ID, since it involves shoting civilians, something we consider ourselves above, since they are the victims of the Alliance's political goals.
We have tried the old subterfuge and political machinations in the past (see:GRU), but generally, anything attempted in such a fashion is either seen as rule-breaking, or is simply power-played out of.
As regarding the Order, the Phantoms are friendly to Corsairs in spite of being hostile to the Order. The Order also get on well with the GMG, who are hostile to their allies in the Corsairs.
We aren't a threat to humanity in the sense that the Nomads are, we're a threat to the existing political structures.