@Fuminino
Francois were dependant on a very stringent interpretation of the laws and the Empire upholding them as the main part of their strategy.
The Empire essentially gave them a short-timed choice : 1) Uphold the laws you're exploiting and immediately give up your plan or sacrifice your civilians for it or 2) Ignore the loopholes you're exploiting and press on, hoping the Empire would value a rebellious bunch of citizens over their own troops at the frontline or 3) Atleast keep control of your own troops and keep from committing further war crimes which would give the Empire more reasons to take drastic measures to deal with your plan.
Francois could've evacuated the troops, and removed any visible signs of partisans / militia, which might've avoided the bombardment until they act up again.
Francois could've evacuated the non-combatants as they were legally obligated to do, unless they wanted to actively use them as meatshields, which would've removed most civilian casualties.
Basically, if your entire strategy is about using your own citizens as both meatshields and partisans and hoping the enemy would only consider them as civilians, and not come up with an equally exploiting method to deal with your loopholes, it's a very limited plan.
@cryum
Or the Empire's ability to... legalize the way they dealt with the situation.