I don't get how Archer acts at all in that episode... "What gives you the right to take prisoners?" "Well they were trying to attack us and steal our stuff..." "But you'll make the Naussicans angry" "Angry enough they'll start attacking our cargo ships?"
Starfleet clearly wasn't defending the Earth Cargo Ships, as the episode clearly states Enterprise is the first long range ship and responding to a distress call so far out is something new. So if they don't take care of themselves, who's going to?
I think it was Sfdebris who called this the "Archer Maneuver" siding with your enemies against your allies. Archer should have taken the Naussicans into custody and taken them back to Earth for trial and get on the phone with Forrest and get him to start raising hell with the Naussican government over this one.