We've taken 4 cruises from the Port of Los Angeles in San Pedro. (Only one to Mexico) I'd tell your wife to be in the last group off the ship to use up some time.
I don't see how you can get to her in an hour or two if you have to get to an airport in Mexico, fly to LAX and collect your bags, shuttle to the car rentals, and drive down to SP.
I agree with 55vineyard about walking or taking a cab to the Grinder Coffee Shop, where she could sit. I also like the Crown Plaza near by, where I'm involved in a Fashion Show Luncheon every year and enjoy the facilities. There is a nice lobby to sit and wait or just off the lobby is Blu Restaurant, open at 6:30 am for B or L.
I personally would avoid Port's O Call. It's not what it used to be, too crowded to be saddled with luggage on a Saturday morning for waiting around. However, we go to the Crusty Crab and SP Fish Market on summer evenings and enjoy it.
Did you ever think about renting a room at the Sunrise Motel for $75 a night for her, and just having your wife wait there? You don't have to stay there after you meet up, but sometimes it's less stress for the one waiting, especially if there is some delay in your flight that same morning.