I've heard this being stated quite a few times and it makes me wonder - what would the effects on Morocco be if the Nationalists had fled there and transformed it into a Fascist state?
I think the effects can be divided into two categories:
Immediate: I don't think there would have much of an effect. The people of Western Sahara holds themselves as being a distinct people from Moroccans. Thus, I don't think there would be much of an immediate interest in exporting an independence movement to Morocco. Likewise, France would of had more than enough strength to contain any independence exports and also to make life very unpleasant for the new nation if they needed.
Later: An early independence of Western Sahara would probably lead to the creation of an identity of distinct nation state. This would probably prevent the annexation of the area by Morocco. Maybe..... Fascist Western Sahara finds a soul mate amongst Lebanese Phalangist groups. This leads to a steady migration of Lebanese (with their customary education and business skills) to Western Sahara.
Also.... Western Sahara is growing. The Canary Islands have just declared independence from Spain and "anchllussed" themselves to Western Sahara. German and Italian naval forces routinely use the islands for re-supply- and their presence puts a damper on any Republican attempts to re-cover the islands. The Axis presence is even tacitly supported by France and Britain as the Republican government lurches leftwards towards communism.
Western Sahara and the rest of Morocco is not viable as a Spanish Taiwan
It might depend on the numbers. I imagine most Rightist refugees would seek a new life in fascist Italy, or quasi fascist nations in Latin America or Cuba. But.... a few would have ties to Western Sahara via business, or former military service. The region could absorb these few.