i haven't been there, but apparently Bistro West offers a separate GF menu and the items are prepared in a dedicated space in the kitchen. and West Steak & Seafood (owned by the same people, i believe) has a really extensive GF menu.
there's always Naked Cafe...and Broken Yolk now offers GF pancakes, though i have no idea if they take any steps to avoid cross-contamination.
for higher-end, the California Bistro at the Four Seasons Aviara.
if you're willing to travel south a bit, there's Lotus Cafe in Encinitas and Ki's in Cardiff.