Even if being kind to bystanders is not a military priority in its own right, there are surely three good military reasons for preventing individual plundering:

1, that a hostile population can be dangerous;
2, that it made collecting official contributions difficult, which Napoleon did complain of;
3, that troops which scatter to plunder are difficult to control.

There is also the difficulty of transporting the loot once it is collected - as in Russia.

The Directory had a big drive to remove dishonest generals in 1799 but it caused so much unpopularity that the relevant Directors got removed instead. I would have thought Napoleon was in a rather stronger position.

regards,

Susan