Found this in Memoirs of Admiral Sir Sidney Smith, K. C. B., &c: Volume 2 by Edward Howard, William Sidney Smith 1839:pg. 404-405.
It is supposed to be the translation (original in Arabic) of N's proclamation upon arriving in Egypt
". . .Our friendship shall be extended to those of the inhabitants of Egypt who shall join us, as also to those who shall remain in their dwellings, and observe a strict neutrality; and when they have seen our conduct with their own eyes, hasten to submit to us; but the dreadful punishment of death awaits those who shall take up arms for the Beys, and against us. For them there shall be no deliverance, nor shall any trace of them remain.
Art. 1. All places which shall be three leagues distant from the route of the French army, shall send one of their principal inhabitants to the French general, to declare that they submit, and will hoist the French flag which is blue, white, and red.
Art. 2. Every village which shall oppose the French army shall be burned to the ground.
Art. 3. Every village which shall submit to the French shall hoist the French flag, and that of the Sublime Porte, their ally, whose duration be eternal.
Art. 4. The chiefs and principal persons of each town and village shall seal up the houses and effects of the Beys, and take care that not the smallest article shall be lost.
Art. 5. The Shekhs, Cadis, and Imams shall continue to exercise their respective functions, and put up their prayers and perform the exercise of religious worship in the mosques and houses of prayer. All the inhabitants of Egypt shall offer up thanks to the Supreme Being, and put up public prayers for the destruction of the Beys. . ."
Assuming this is legit, then it would seem that the obvious reason that the garrison at Jaffa was executed is that they took up arms in defense against the French. Once Napoleon promised destruction and death for all with any resistance, he had to deliver.
This ruthless behavior -according to reports- backfired on the French in that it helped to inspire the defenders of Acre; where Napoleon suffers his first serious defeat and stops cold Napoleon's Oriental ambitions.
My view is that the ultimate undoing of Napoleon and the French Army was this ruthless behaviour when -as a matter of standard procedure- they used terror tactics on the various populations they endeavored to conquer; which was above and beyond the also always present tactic of "living off the land."