If a Retainer is a ghoul, must I have a higher level of a Discipline than the ghoul for the ghoul to fully specialize in that discipline? Take, for example, a Brujah with 1 Celerity who buys a 3-point ghoul Retainer. Can that ghoul have 3 Celerity?

No, your character does not need to have a higher level of a Discipline than her ghoul. Your ghoul can learn one Discipline by itself as long as it has blood that’s capable of manifesting that Discipline. Therefore, in your example, the Brujah’s ghoul can have 3 Celerity even though its domitor only has 1 Celerity.