As a matter of fact, the treaty of Tordesillas defined the zones of Portuguese and Spanish influence in Morocco, being the Spanish area limited to the Mediterranean coast (this sphere of influence reflected much the border of the 19th-century Spanish Morocco). That being said, Portugal is in the best position to occupy and control Morocco. Heck, the Portuguese king even styled Morocco as Algarve of Overseas.
As you can see in the map, the Portuguese were much more succesful than we actually think they were. IMHO it was the Iberian Union that demolished the project of a Christianized Morocco. As I see it, the Portuguese can concentrate much more resources in North Africa than the Spanish, as the Hapsburgs have other concerns both in Europe and in the Americas. Also, Portugal can and will avoid unneeded rivalry with other European powers, such as France, England and the Netherlands (the English notably provided weapons to the Moroccans to fight against the Iberian Union). Of course, there will always be the problem of having an important population densitiy and the eventual Ottoman support will always be a probability, but with some luck I think that Portugal can slowly conquer the entire country.