I think there is a bit of a burden of guilt on Jack's part over the fact that the Enkarans are facing extinction on the planet we selected for them. Not to mention the fact that they can only save the population of one village if they do evacuate. Hardly conducive to the continuation of a species if the gene pool contracts that small.
Given that they have so little time, and even with that they can't save everyone, it doesn't surprise me in the slightest that Jack's response is to go for the quickest, military solution. He doesn't feel he has the time to phutz about with negotiations - not when there are so many lives at stake.
On the other hand, Daniel was lucky that he could get through to Lotan. Not everyone is so accommodating. Had Lotan had less 'self-autonomous' artificial intelligence, then it may be that his programming would simply not have allowed him to deviate from his mission, no matter how many people would die as a result.
But, I agree, it's an interesting moral dilemma - and testament to what can be achieved if everyone at the negotiating table is prepared to compromise for the best (or, possibly, least worst) solution.