I'm not sure if FreeSpace itself was subject to this backlash, but other stuff which used similar names was. Volition might have decided to be on the safe side and avoid all possible criticism and just use more neutral names.
Interestingly though, this decision appears to have been made sometime during development, as if you take a peek into the mission files of FS2 some of them still refer to them with their original names, albeit behind the scenes (like message or event names, invisible to the player).
Also, NTF ships were originally named "Marauder" and "Bandit" as if they were Pirates like in Derelict. You can still see a remnant of this in the Sixth Wonder briefing (one of the bomber wings being named "Bandit").