It appears that you are not familiar with the French use and application of their military justice system. Perhaps the following will help.

In 1796 the Directory, after multiple changes and much confusion, established Permanent Councils of War (a court-martial), comprised of seven members, in every division of the army. The president of the council was a chef de brigade (colonel) assisted by one chef de bataillon or escadron, two captains, a lieutenant, a sous-lieutenant and a noncommissioned officer. All of these members were appointed by the division commander.

One of the captains would be appointed by the president of the council as the prosecutor (commissaire du pouvoir) and the other as the court recorder with a clerk appointed to assist him. The clerk was not appointed by the division commander but chosen by the council.

If a senior officer was being court-martialed, the composition of the council was changed to reflect his rank and would include officers of equivalent grade and time in service.
These courts had jurisdiction over troops, civilians with the army, spies, inhabitants of occupied countries, and embauchers. They had the authority to impose any sentence that was deemed appropriate, including death.

In 1797 Permanent Councils of Review were established in the divisions which were to review the sentences of the Permanent Councils of War. These too were appointed by the division commanders and when they reviewed a case, what was considered were the procedures of the trial. If those were deemed to have been conducted correctly, the sentence would stand. If not, then a new council of war was appointed for a new trial. If a different verdict was reached in the second trail, the case was then referred to the Corps Legislatif.

This system was designed to function only during wartime. In 1800 First Consul Bonaparte ordered Berthier to report on the military justice system, along with all pertinent and supporting laws and regulations that went along with it. When the Treaty of Amiens and peace came in 1802, the First Consul ordered that the system be continued. There would be only minor changes to the system until 1857. Le Guide des Juges Militaires was published in 1813 which covered in detail, including laws, acts of the government, decisions of the Council of State, along with a listing of crimes and punishments, which applied to military and naval legislation and the military justice system.

Special courts-martial were established to deal with crimes committed by refractaires, spies, embauchers, and deserters outside the pruview of the field armies. The legal authority of the governors of fortified places during peace, war, and while being besieged was ‘redefined’ in 1811. If under siege, the governor of a fortified place had the power of life and death and the civil courts in the place had no authority at all.

There were two other military courts. The first, the gendarmerie’s tribunal prevotale and the commissions militaires, which was a drumhead court-martial. There was no appeal from either of them.

The tribunal, in essence a summary court-martial, was authorized to try any crime committed within the army. However, most of its legal business dealt with the army’s camp-followers. Troops that were caught committing serious crimes were usually turned over to their regiments for court-martial.

The Grand Prevot, the army’s provost martial would ask for the immediate establishment of a military commission to try egregious looters or marauders.

The commissions dealt with stragglers, deserters, and marauders. Both of these special courts-martial had jurisdiction over any and all criminal activity and were authorized to use the death penalty.

Military juris prudence was somewhat advance in the Grande Armee, and there are many similarities with modern military justice in the American services. There is a table of maximum punishments in the Uniform Code of Military Justice, and the death penalty can be applied for such crimes as murder and rape, among others (the current prisoner in custody of the US Army, Bergdahl, most certainly is eligible for the death penalty, although unfortunately it won’t be applied). I’ve had some experience with the military justice system as both a staff officer and a commander, being on a few court-martials (special and general) and applying punishment both on land and sea, the latter including putting recalcitrant on bread and water while deployed aboard ship. It’s a very interesting system and process.

The death penalty in the Grande Armee was the punishment for ‘attacking or threatening an officer, NCO, or gendarme; desertion to the enemy; theft with violence; rape of a woman of good repute; and murdering a wounded enemy officer and stealing his medals.

Punishment for ‘lesser offenses’ could be handled, then as now, by the units, usually at the company and battalion level. Many times it is up to the imagination of the company/battery 1st Sergeants to come up with suitable punishments that are not referred to the commanding officer.