You wrote "Didn't Smith invoke Bonaparte to desert his army..."
Only indirectly, I think Smith knew that B. would not be responsive to anything that he -Smith- might suggest.. it would probably provide negative results. What Smith did was very sly, he just slipped in a couple of newspapers along with some other papers without comment. Probably tried to make it look like an accident. If B. got even a sniff that Smith was up to something, he might have thought longer about what he was doing. As I recall, N. was later recorded as saying that he would have been better off staying in Egypt.
Remember, it was something like a year that there was no news from home. They had no idea what was going on. When B. read that France was going to hell without him..... as Smith knew would happen, B. left his army.
The motives of Smith to do this? I'm not sure that he ever wrote about that. My guess is that Smith thought he might get lucky and catch him trying to escape. That B. managed to escape without getting caught has, I suspect, brought up the theory that Smith intentionally wanted B. to make it to France (review of the new book "Bonaparte" mentions something to this effect.)
Part of Smith's propaganda campaign -yes, he intended from the outset to use propaganda against the French- was to print flyers offering any French soldier immediate and safe passage back to France: of course they would first have to desert. Now would Smith have honored this pledge if B. showed up on his doorstep? Not sure. Probably would have if it included the entire army at the same time. Of course, that would have resulted in B. looking like a loser and that certainly would not have been acceptable to him. Don't think he really any choice but to sneak away in the night. And sneak he must. Chances are that any ceremony or even the knowledge that he was ready to go would have resulted in his capture by the Brits.
Another part of Smith's propaganda campaign was when he came into possession of the proclamations N. had made (remember Smith had undercover agents capable of moving behind enemy lines) and problem was that the proclamation to the Islamist said one thing and his proclamation to the Christians said something else. Smith simply reprinted these and distributed copies to the sides that they were not intended for.