My apologies for bringing politics into this. However, Star Trek does have a tradition of episodes commenting on or paralleling political events, and to me this parallel seemed quite strong.
For some reason, I saw the episode as a commentary on the US invasion of Iraq. Substitute the initial 'sub-quantum transportation' for 'Weapons of Mass Destruction' as the initial goal(with Archer/Enterprise representing the US citizenry/army) and 'rescuing Erikson's son' for 'establishing Iraqi democracy'.
I think the parallel works quite well, especially considering Archer's decision to continue over Trip's opposition. The ending too is quite thoughtful, with its questions of whether the results were worth the cost.
I think the parallel also works because it didn't side overtly with one side or the other, reflecting the ambivalence over the Iraq issue.