I’ll also second the Golden Gate. You could combine two activities and ride bicycles across the bridge (though the weather in the spring can be hit-or-miss). You could make an entire day of Golden Gate Park: The De Young, the Japanese Tea Garden, the Arboretum, etc, etc, etc.
SFMOMA is free the first Tuesday of every month (but tends to be busier than other days, obviously)
If you do Alcatraz, try to get a night-time tour. They tend to go into more depth than the tours during the day. And you get to see the City at night, which is breath-taking (assuming it’s not fogged in).
If she’s coming from anywhere without a western coast, Sunset at Sutro Baths is a great thing to do.
Angel Island / Sausalito Ferries? At the very least, some time wandering around the Ferry Building.
If you have access to a car, Muir Woods. You might also consider Berkeley, do you think you could convince her to take the Scharffenberger tour (in Emeryville? ;-`) I don’t remember if that’s BART-able.
I don’t know how unadventurous she is, but I’d strongly recommend at least one burrito in the Mission while she’s here. Burritophile can hook you up with more suggestions than I can off the top of my head.
Ok, I’m sure I’ll think of 10 other things as soon as I answer this, but I’ve babbled more than enough.
EDIT: Can’t leave well enough alone. One thing you might consider is one dinner at a fancy, quintessentially California restaurant: Chez Panisse, Millennium, Greens, The Slanted Door (though this one might be too “weird”). You’ll get excellent food that may push some of her boundaries, but surprise her: we took my “what are the carnivores going to eat?” father to Millennium once, and he still raves about it.