The three options seem to be:
a) The Swiss have to take him into custody "for his own protection" and hand him over to the Allies after a token protest, leading to The Trial Of Mussolini
b) He gets onto a plane to Spain which is intercepted
c) He makes it to Spain, and Spain is leaned on to hand him over to the Allies, which Franco does after a token protest
The least likely but most interesting would be if Franco protests too much and the Western Allies open a Spanish front, which completely changes Spanish history from '45 onwards