Although Archer was correct in his suspicion that the repairs were too good to be true for the requested fee, Enterprise had spent the previous year offering assistance (repairs, medical supplies, etc.) to anyone that needed it, and rarely asked for anything of significant value in return.
Archer reprimands Trip and Malcolm for trying to get into the station's computer, stating that they could have been transported out into space. However with the new knowledge that the station has kidnapped one of their crew members, Archer allows Malcolm to repeat the stunt without caring for his safety.