Morocco claims sovereignty on Western Sahara, though it's claims are unfounded, and has illegally seized lands after Mauritania retired their claims on saharan soil. Furthermore, Morocco has proven time and time again to be undemocratic towards this issue by blocking any referendum and refusing to engage into any negotiations whatsoever.
If WS becomes independent it will be plagued by tribal turmoil and foreign interference from mainly Algeria and Spain. An unviable state that's unable to sustain itself where extremist and terrorist group (aqim for example) will thrive by creating strongholds and recruiting cells. An independent western sahara will destabilize morocco a strong ally to the west and major barrier to illegal immigration to Europe. The autonomy plan proposed by Morocco is the answer to the Sahrawi aspiration while an independent western sahara will be nothing more than a burden and a catalyst in the destabilization of the sahel region already a mess.