As it turns out, Omar Ben Ali was quite wise.
Spain could never let go of him as the Caliph; as long as he was alive, the Sokoto Caliphate would, in name, continue to exist.
Once he died, Spain could abolish the title of Caliph, and rightfully bring Sokoto into its domain of control.
As long as the entire Sokoto was under Spain's colonial rule, no matter how brutal Spain might be, they wouldn't completely wipe out the indigenous people of Sokoto.
After all, European countries pride themselves on being representatives of civilization, so they must maintain appearances. Historically, Belgium didn't do well in this regard, and the eventual result was European Powers intervening forcefully, to prevent Belgium from further damaging the image of the European countries.
Examples can also be found from Spain's rule over other colonies. Throughout Spain, there was a pervasive disdain for blacks, and blacks were the only race that could not obtain Spanish nationality.
