My main goal in doing this ourselves is to get a real idea of what Bonaire is like and what the diving is like not to be thrown on and off a boat on the closest reef to the ship!
Tight schedule - if you work at it, you should be able to do 2-3 dives - and squeeze in a little lunch also.
The only holdup being the orientation. fwiw, we dove Bari Reef w/BD&A, then moved 2 min down the street and dove Cliff and LaMachaca at Capt's Dons all from about noon-5pm. Call a cab when you get out of the water between dives, they're close by physically but at least a 1/4 mi. walk since you have to go back out to the road to go between properties, and they all run perpendicular to the road in that area.
Actually being thrown off the closest reef in Bonaire would be a good thing.
Since that's the world famous Town Pier. Where your ship will tie up. Too bad it's only dove at night - right after your ship is gone.
Any dive resort on Bonaire is situated directly offshore from the reef, in some areas it's as close as 30' or less to the coral(literally). None of the resorts are more than 5-10min. from the cruise dock.
The problem with the orientation scheduling might be that they may not be ready to do it for you on arrival without prior notification. The standard practice on Bonaire is to arrive later, do the orientation first thing the next morning and then dive all week.
Recently there's new early a.m. flights to there, so there may be more diveops doing afternoon orientations now. We stay to the south in a condo, and had our own private orientation the next morning after we got up (long flight) probably around 11 or so. Just us and the instructor, it would have taken 15mins. except my buddy did his Nitrox referral that morning.
Most of the diveops on Bonaire have smaller boats so the likelihood of being on any sort of cattle trip, especially in the afternoon is slim to none. Capt' Don's and Buddy Dive have the only bigger boats on the island, up to about 36' or so, BD&A's are around 20' or slightly more - the type with open bows and canopy tops.
Another option might be WannaDive, they're pretty accommodating. imo, everybody I've dealt with there is, Capt' Dons less so - the only resort that's $5 to dive there if you're not a guest.
hth,