One the cases Sandel discusses (in his book and in the talk he gave at VMI) is that of Marcus Luttrell. Luttrell was searching for a Taliban leader in Afghanistan with a team of SEALs when their position was discovered by some local goat herders. Sandel tells the story (as Luttrell seems to too, judging by this Wikipedia article) as though Luttrell and his men faced a simple choice: kill the goat herders so that the Taliban would not find out about their presence in the area, or let them go and risk being found and attacked (as in fact they were, all but Luttrell being killed, along with a rescue team in a helicopter that was shot down). It is easy for soldiers and soldiers-to-be to come away thinking that killing the goat herders would have been the right thing to do.
But it isn't immediately clear why tying up the goat herders would not have been an option. Perhaps rope and gags should be taken on such missions just in case. I've heard, though, that in this case that might well not have worked because the goats walked the same route every day, and would have carried on back to their village without the herders. This might have given the game away too. As, presumably, would killing (or tying up) all the goats. So it looks as though the only options were to let the herders go and carry on with the mission (which was very risky) or else to let them go and abort the mission. Murdering the goat herders might well have been suicide (not literally) as well as murder.
The presentation of the situation as a moral dilemma (kill or be killed) is not true to the case. It also encourages murder in future similar cases. Which seems like a bad idea.