If I believed that you, in all seriousness, wondered if they ever thought deeply about such things, I wouldn't have said anything. The only thing "have you heard of 9/11" says to me is that the individual feels attacked by you. Given all the words you have written here, I think it is reasonable for them to interpret your question as an attack and not some good faith attempt to start some deeply philosophical discussion.
And it's an ugly thing to do, regardless of the justification you want to come up with after the fact while clearly signaling your belief that being a soldier makes you de facto evil. I don't agree with that position and I don't think it is appropriate for anyone to go around picking fights with soldiers on HN because they hold such beliefs.
You are required to follow legal orders. Illegal orders, not so much because "you will end up holding the bag" as "I was just following orders" isn't a valid defense.
As for net positive/negative that really up to the politicians since (in the US at least) the military is commanded by the civilian government. One hopes one is engaging in a net positive but, as they say, hindsight is 20/20.
Have a read:
You don't own this entire thread because you spoke in it. I'm quite open about my background. It should hardly come as a shock to you that I don't agree with the idea of personally vilifying military members because you personally disagree with the politics of their country.
Anyway, I'm done, regardless of whatever else you want to say here.