Deputy sheriffs are legitimate law officers, with all the powers of arrest as a police officer. It seems to me that, in larger metropolitan areas, sheriff's depts. often seem more in the background. One problem you might run into is that if the police dept. and sheriff's dept. are well connected (buddy, buddy), the sheriff's dept. might automatically refer you back to the police dept.
How high up does this 'friendship' with the ex's father go in the police dept.? If it spills over to other area LE agencies, you may have to go to the state atty. general, who is the governing body over all state law enforcement, if nothing else but to report the discriminatory actions of the dept. Keep in mind that many LE agencies will not get involved with custody orders (saying it is a civil matter) but when you have a specific order for pick up, they should be able to assist at least as standby.