We've been to Bonaire 3 times and stayed at Sand Dollar. Our experience with BD&A has been excellent and the house reef, Bari Reef, is absolutely fantasic day and night. After a little expereince post certification, the reef would be a great place for you and your wife to dive independently. The orientation can be quite tedious, especially if led by Andre. Repeat visitors can take a short course that is far less painful. The dive with the naturalist course with Jerry Lignon should not be missed, one of the most valuable training experiences I've had. The DM led boat dives from BD&A are ideal for a newly certified diver gaining confidence.
Ex-BD&A employee, Wietze Koopman, really is extraordinary. He is now at Bonaire East Coast Diving (ex-Larry's Wild Side). I would highly recommend at least a day of diving on the East coast for a real change of pace. This may not be a dive for your wife soon after certification.
BD&A is directly downstairs from Den Lamen, personally, I would take advantage of the convenience and dive with this very good operation.
Good diving, Craig