Archer does the right thing. These guys gotta protect their cargo, not take prisoners, mistreat them and make the Nausicaans do more than just take their cargo.
Taking the prisoner wasn't wrong. As I said previously, the alternatives are to kill him, or let him rob you blind. Both seem worse. Archer doing the right thing though? He escalated the situation with that silly threat to remove all the components they installed when he should've been trying to talk the Fortunate down, and take the prisoner(who by maritime law is a pirate) until Starfleet can establish diplomatic contact with the Naussicans and sort this out.