This Spanish documentary aired on History Channel seem to disagree with that view...
http://www.youtube.com/watch?v=fxwjh-S1CQY
Apart from that Francisco Franco already had a preference for RM way before the late 1950's claiming otherwise is just stupid plain and simple (and changing history).
"In 1936, when Francisco Franco started the golpe against the democratic Second Spanish Republic, the president of Barcelona FC Josep Sunyol was arrested and executed by Franco's security police[8] (Sunyol was exercising his political activities, visiting Republican troops north of Madrid[9]). The Barcelona FC was on top of the list of organizations to be purged by Franco's troops, just after Communists, Anarchists and Separatists.[8][11]" (several references and firsthand sources in those references used, 8, 9 and 11) (El Clásico article on English Wikipedia)
Whether there was any involvement from the fascist government in the 11-1 defeat or not is not known for sure.
The only thing that is sure is that FCB won the first leg 3-0 at home to lose 11-1 away in the return leg a week later. Most people would find that strange....
What is certain is that the preference of Franco was clear and that is a undeniable fact although some madridistas try to paint a different image.
Leading 8-0 after the first half (after having lost 3-0 away) can hardly be seen as normal as you try to make it out....