I have looked into this during my study of Macdonald. If I can quote from my own work this is what I found out about his command in Naples in 1799:

>'I published proclamations, backed up by effective demonstrations', says Macdonald: on 4.3 he published a long proclamation intended to repress insurgent activity, it was a variant of the one he had issued in Rome and has attracted a great deal of criticism.
Among the provisions we find that (Acton) ‘Every district or city in rebellion against the republic shall be burnt and levelled with the ground;Cardinals, archbishops, bishops, abbots, parish priests, and all ministers of public worship shall be held responsible for rebellions in the places where they reside, and be punished with death;
Every rebel shall be liable to pay the death penalty, and every accomplice, whether layman or clerical, shall be treated as a rebel.”
‘the death penalty also applied to priests in whose parishes a double peal of bells were rung, and to those who spead news adverse to the French or the Republic.’
7.3 (Di Nicola's diary) 'A terrible proclamation from the General against those who spread alarming rumours or promote tumults etc. Order that when the alarm is sounded all citizens must retire indoors, that the priests are responsible for keeping order, ringing the bells as an alarm is forbidden; hunting is forbidden until further notice; all under penalty of death. He promises security and protection of cults and their ministers.'
The English Navy got a copy later: 'A curious proclamation of Macdonald's was at this time brought off to us; it threatened death to any who sided with their rightful sovereign, or the English, and made the bishops and priests answerable with their lives for the consequences of any insurrection or tumult that might arise in their districts. At the time this sanguinary proclamation was issued an insurrection against the French usurpers took place at Trani..... But the French having soon made themselves masters of the place, put all the men to the sword, and then, in cold blood, shut up the women and children in a large house, set it on fire, and consumed them all!'

The publication of this effectively placed the entire kingdom under martial law, rather negating the power of the republic, but that was only a recognition of the facts. 'Terrible' and 'sanguinary' as the orders are, they were within the laws of war of the time and were aimed at frightening neutral towns into surrender. In hostile towns the ordinary laws of war, which state that a place that resists once a breach has been made in the walls can be sacked, were already in operation, in which case the death penalty was being imposed without any enquiry into guilt or responsibility. It is not clear how many people were ever convicted under this edict, the only example I have found is '12.3 A military commission of the first division, General de brigade Calvin presiding, to try suspected insurgents at Pagano. Two were found guilty, one acquitted, the death penalty was imposed.'
Thiebault heard that Sarrazin had had 130 men shot as suspected chiefs of the insurrection 'the idea appeared to me simply infernal.' Di Nicola reported 10.4 'This morning at 10 hours French, 11 men condemned as traitors to their country (as the notice fixed up said) were shot in the market place, having caused an insurrection in Torre. The criminal lawyer who undertook their defence believes they did not deserve death and that this is more an example of terror than of justice. The place was surrounded by civic guards and Michele il Pazzo harangued the people, instructing them of the example.' These men had been condemned by the revolutionary court, not by the army.

There is little evidence that the army was bothering with the finer points of law:
(Poles) In the night of 4-5 germinal (24-25 march) a column under general Watrin , including a detachment of Poles, marched against Traeta, which was taken at point of bayonet after vigorous resistance. 'Nearly 1200 rebels died there, the town was burned and the ramparts rased.'
Watrin left the Poles at Traeta and marched on Castel-Forte, which he carried by force, 'the town was given over to the flames and the walls equally destroyed'. The Polish legion lost heavily in these affairs.
Monitore: In the Garigliano have been burned Castelforte, Itri and Trajetta.

What can be said is that Macdonald was in favour of a less bloody approach, the Monitore published a letter from Ettore Carafa, commanding a legion of Neapolitan troops reporting to the president on his successful campaign in Montefesco province. He had marched on Montuoro sending 'a terrible proclamation', which led to a request of peace. The townspeople had offered a patriotic gift to the whole troop and promised to lay down their arms.

He reported to Macdonald who replied,
HQ Naples 9.3
"I have received your letter in which I am informed of the disarmament of Montuoro.'
I understand with the greatest satisfaction that you have used courage and prudence in this campaign, which enhances your glory and that of the citizens who have enrolled under the flag of freedom. Receive on behalf of the country the tributes of praise which you deserve; you have fought for it, its genius protects and constantly watches over you, we have obtained a victory which leaves us with no other regrets than the loss of two men.
I approve all conciliation agreements made by you and everything you promised. We must show the people who have been led astray that the Great Nation, though terrible to its enemies, is equally generous to those who return to their duty."

This is an example of how a 'terrible proclamation' was supposed to work and demonstrates Macdonald's intentions.<

When the French returned to Naples in 1806 Napoleon's advice to Joseph is worth noting: April 1806 "I am glad to see that a village of the insurgents has been burnt. Severe examples are necessary. I presume that the soldiers have been allowed to plunder this village. This is the way to treat villages which revolt. It is one of the rights of war; but it is also a duty prescribed by policy." July " Besides this you should order two or three of the villages that have behaved the worst to be pillaged; it will be an example and will restore the gaiety and the desire for action of your soldiers." "Grant no pardons; do military execution on at least 600 rebels; they have murdered a great number of my soldiers. Let the houses of thirty of the principal heads of villages be burned and distribute their property among the troops. Disarm all the inhabitants and pillage five or six of the large villages which have behaved worst." August "I am waiting to hear how many estates you have confiscated in Calabria, and how many rebels you have executed. You should shoot in every village three of the ringleaders. Do not spare the priests more than the others." "I should like very much to hear of a revolt of the Neapolitan populace. You will never be their master till you have made an example of them."

Susan