With no PoDs prior to 1806 (and without touching the events leading to Tilsit), how can Spain remain both stable and an ally for Napoleon (part of his Continental System, etc)?
Can the fall of Manuel Godoy and/or the Abdication of Charles IV be avoided? If not, could the disasterof the Peninsular War be avoided? And I do realize the answers will involve the question of Portgual; if avoiding the Treaty of Fontainebleau helps, how can that be done?
Give him some reason to doubt his use of force and the long term effects of the necessity to use armies to enforce his will. Napoleon was never going to learn until he had a few setbacks, and the little setbacks never deterred somebody like him.
One way of extinguishing the Spanish issue is to not have overt actions taken deep into Iberia (leaving Dupont in trouble?, Junot being cutoff ?), perhaps by making him realise the problems with transportation and logistics; there was a trial run with guerillas in Calabria.
Or, get someone close enough to him who would be able to push him. Convince him that French interests can as easily be take care of by allowing local factors to take shape, only then should he shape them (like using Godoy until he became unpopular).
Once he had decided to push his brother on to the throne (one which Joseph did not even want to take instead of the crown of Naples) and the insurrections started, it became a matter of face for Bonaparte. A turn about in policy would be equal to saying that the rebels (all forces in opposition to King Joseph) had won.
Had Spain not been meddled with, Wellington would have remained in Portugal's tip or been forced to disembark later on.