This would have to be done after the main(startup) pilot selection screen; AFAIK, people don't switch to a fresh pilot file before quitting and changing mods(you select the mod, start FSO, make a new pilot, and go from there).
Therefore, any automatic switching done before the startup pilot screen will probably just cause unwanted reseting of pilot files for other campaigns(whatever pilot was left selected when you last played), and also may not have any effect on cloned pilots made at the startup pilot screen(I for one, use modified joystick mapping, and thus reclone my main FS2 pilot file whenever I start a new pilot for another mod, to keep those controls).
An in-game check/pop-up just like the 'new user tips' that appears by default on the main hall for newly-created pilots, would be the ideal, I think. Either that, or introduce pilot management abilities(create/clone/select) into the Launcher, so all needed switching and prompting can be done out-of-game, at the time you're switching mods.