...A military officer may not completely agree with what his command officer is doing, but as he has chosen to be a part of that military structure, when he is killed by enemy forces, they are justified in their actions.
Agreed.
The nobles have put themselves in a position where they are targeted due to the society that have helped uphold....
Agreed.
...If there are two groups of people, and one group starts attacking the other, am I in the wrong if, while fighting back, I injure people who were with the group, but had not necessarily been the ones to attack me? Perhaps more caution should be taken, but they had involved, and continued to involve themselves with a hostile force.
Agreed.
You clearly point out why killing Skaa and killing Nobles are not equivalent acts.
To transpose this on the real world...there's a fuzzy line, especially in our age of representative governments, between those who are responsible for objectionable acts performed under the umbrella of a government and those who are not. To give it a face in Palestine, in my opinion any given Israeli soldier is a legitimate target for the Palestinian "resistance." His family is not. Random people in a marketplace are not. The same goes for Iraq. Any given soldier, American, British, Iraqi, etc... is a legitimate target for the "resistance." The children surrounding a candy giveaway, or worshipers at a mosque are not. There's definitely a fuzzy area in between the two extremes though.
I think Nobles in the Mistborn world fall on the killable side of the line. Do their young children? I don't think so. Did Kelsier kill noble children on purpose? I don't remember. Moral justification aside, I think the question of craziness on Kelsier's part rests on that point. Did he indiscriminately murder anyone of noble blood? Did he target Skaa servants of the nobility? The more indiscriminate he was, the crazier he gets in my opinion.