Yes you may make combat maneuvers with prehensile hair
Page 199 Core Rulebook: When you attempt to perform a combat maneuver, make an attack roll and add your CMB in place of your normal attack bonus. Add any bonuses you currently have on attack rolls due to spells, feats, and other effects. These bonuses must be applicable to the weapon or attack used to perform the maneuver.
Combat section: Attacks with secondary natural attacks are made using your base attack bonus minus 5.
So the combat maneuver check, which is an attack roll, specifically says incurs the penalties made on attack rolls. Thus you would make the attack roll with your CMB but incur the -5 penalty.
The witch can manipulate her hair as if it were a limb with a Strength score equal to her Intelligence score, thus you would use your intelligence in place of your strength in the CMB.