With DC that age I would do just the zoo. Safari Park is farther north than your other activities, and I think it is better for older children/animal lovers. You wouldn't do both on the same day for sure. They are 40 minutes apart with no traffic (which is never).
Seaport Village is a quaint area, but I'm not sure how interested your young ones will be. They might like to see the boats all along the harbor area.
The zoo is located in Balboa Park, which has lots of other things to do. It's been a while since I was down there, so hopefully some San Diego folks will chime in with more ideas.
I don't know of any deals; we go to SeaWorld every year under their military deal.
I never have been to Scripps or LJ Cove, so I'm no help there.
Be sure to check the weather forecasts. San Diego has microclimates. It might be 70 degrees at SeaWorld (yes, even in August sometimes) and 95 at the zoo at the same time. Or not. Be prepared with light layers.
Have a great trip! We love San Diego.
DS '04 "Boogaboo"
DD '08 "Lilybear"