I am not sure we can ever discuss history without making some moral judgements and while we have to be careful not to be judging by 21st century standards it is important to try and establish what the standards of conduct expected at the time were.
Given that the rules of war allowed civilians who took up arms to be treated as brigands and shot, it is a small step from there to shooting every adult male in a place which has resisted attack. It was done, but not necessarily approved of at the time - Thiebault recorded that in Naples in 1799 Sarrazin had 130 men shot as possible leaders of an insurrection, he called it 'a simply infernal idea.' When one looks at the atrocities carried out in war it becomes very difficult to start apportioning blame except in extreme cases because so much of it was just 'c'est la guerre!'. Ultimately the real blame lies with those who start wars and even that can be hard to determine.
However, some sense of proportion is called for - it is incongruous to justify the massacre of 2000 Arabs yet be outraged by the legal executions of a few generals in 1815.