Let the Nomads, who are meant to be scary scary aliens according to Freelancer, be able to do good amounts of damage when in small groups.
I personally see the Keepers as the 'elite' Nomads in a way. While I know there is no hierachy as such in Nomad society, the Keepers appear to have the greatest freedom across the species as a whole. Plus they are the player faction.
My theory is simple:
Do let the Keepers do a little bit more damage than normal human weapons let them (5% extra say, as these weapons are or so)
Do not let the Nomads do a little bit more damage than normal human weapons let them.
Aka, tone down the NPCs. Keep the player stuff the same.