The Cuban govt would not allow Juan Miguel to stay, thus it was one or the other. I firmly believe that if given the chance to act freely, without fear of repercussions, Juan Miguel would have chosen to stay here with his son.
Remember that Juan Miguel had previously applied for a visa to come here on two occasions prior to Elian's rescue. and that Juan Miguel had called the Miami family in advance to let them know Elian and his mom were on their way.
I know this from speaking personally to the Gonzalez family here in Miami and they have the phone records to prove it.