If low vis is going to freak you out, you might want to re-think your San Diego scuba plans. I have done a fair number of dives here in San Diego that had less than 10 ft vis.
I try to avoid doing dives when others are reporting 5 ft vis or less. Average visibility at La Jolla Shores (where you'd be doing your cert dives) is 10 - 15 ft.
The only thing that would hold me back from diving in a quarry is that there's probably nothing more interesting than bottom-feeders (fish) lurking about. (I'm prepared to take back that statement if someone can provide evidence to the contrary.) Ocean dives are fun because you'll never know what will stop by to make a guest appearance. I think a quarry would be an excellent place to learn how to dive, though. It's cold, dark, and offers low visibility conditions. Such conditions would encourage good buddy skills, develop strong navigation skills, and allow the student to appreciate the special considerations of wearing tons of neoprene. Getting certified in those conditions should serve as a confidence boost to the diver. Warm water, good vis diving should be a piece of cake after quarry diving.
That being said, there's nothing wrong with doing your referral dives in San Diego or somewhere in the Caribbean. It's really up to you.
There are many things to do in the San Diego area while on vacation. Scuba diving is just one of them. I encourage you to do some research online. There's paragliding at the Torrey Pines Glider Port, wine-tasting in Temecula, the Wild Animal Park, Old Globe Theater plays, the zoo, Sea World, exploring tidepools, surfing, sailing, hiking, running on the beach, just hanging out at the beach, driving out to Joshua Tree, checking out the Gaslamp night life, sushi, fish tacos, and the list goes on.
