Avner's (the main character) problem was the way in which he and his team was treated by their Mossed handlers after the job was done.
He had no issue whatsoever with the killing of the terrorists.
I have not seen the movie, but if it portrays the team as remorseful in any way, they got it wrong, very wrong...
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A few interesting links related to the recently released (pushed up because of the film) Aaron Klein book, Striking Back, which appears to present a more accurate version of the events.
aron Klein Discusses 'Striking Back,' A Look At The Munich Killings, Aftermath
Munich' distorts history-Michael Medved
New Book Takes Issue With Spielberg's 'Munich'
Rival tome snipes at 'Munich' 'Striking Back' says 'Vengeance' botches history
He offered the people on his hit list no mercy but it was a rather detached exercise for them save for the revenge hit on the woman. The aftermath of it was that he had no regrets about what he did only that he didn't see how it had really changed anything. It needed to be done no doubt but the lesson was that terror remained as something that simple vengeance wouldn't cure.
I've seen it. It doesn't but it also doesn't show them as mindless killing machines either. Suffice it to say- they are all absolutely committed to carrying out their mission.