I wonder whether TPTB were intending for this to be a morally complicated situation where Our Heroes aren't necessarily very heroic, or whether they intended it to be a fairly straightforward scenario.
and others are giving the writer(there was only one) too much credit. Piller wasn't trying to create a dilemma, he was making a simple morality play. Unfortunately, he couldn't write a decent one.(incidentally, some members of the cast, like Brent Spiner, objected to the premise and brought it up a few times during the filming.)