I believe as the Commission never officially recognized Magliocco as boss, when they gave the family to Colombo they made it known that the family was to be renamed as punishment for the trouble that the family had caused in the recent months. As Magliocco was only the head of the family for a matter of months and the transition happened very quickly after (or during) the Valachi hearings, the Feds probably just went with "Colombo Family" for convenience purposes.