The price premium for housing in good public school areas tends to multiply if you include all the factors. First, you have to pay way too much for housing. Second, you have to commute at least 45 minutes. Third, your utility bills will be higher for these more inland communities.
If I were looking for an affordable, family-friendly community situated perfectly for working in La Jolla and downtown I would choose Bay Park. The elementary schools are actually quite good, but the middle schools and high school suck.
Consider paying paying for private school from 6th grade on from the money you save on auto/commuting costs, utilities/ housing You can find bay/ocean view properties in areas where you do not need A/C here in the 600K range (and getting cheaper by the month).
P.S. – Regardless of where you end up, I also recommend renting first.