Considering when and where it's written, it sounds like an order for Egyptian officials, not the Army of Egypt. Which would be in line with an expedition that was supposed to bring enlightenment and civilization to Egypt. The last line of the letter says:
"Ce qui n'empÍche pas les agas(Chefs de police) d'infliger la bastonnade, mais seulement comme punition."
So this seems to be relatively limited order (that doesn't even effect the police) directed at the practice of bastonading, or the beating of the soles of the feet of a prisoner in the Egyptian judicial system. I believe torture by such means was a valid means of extracting a confession in Mameluk law. Similar efforts were made to abolish the Inquisition in Spain after 1808.