I also went to Giannini during the late 60's and don't recall any garden at that time. But according to their website, Sunset Community Garden began in 1942 and using their map, it was located just about on the corner of 37th Ave & Pacheco (right about at the top of the sand dune hill where we ran the 880 during gym).
Here is the link: https://communitygarden.org/find-a-garden/gardens/sunset-community-garden-2/
Perhaps there was a period of time when the garden area wasn't active (which could make sense of sorts during the anti-Vietnam war era) as a possible explanation. But considering that a number of hippies of that time later turned somewhat vegetarian to a point and/or otherwise organic-minded, I would think such a community garden would have been active. Then again, I wonder if some of it's "produce" went up in smoke. ;-)
I tried looking for photos without much luck so far. I would suggest keeping a close eye on the new www.OpenSFHistory.org website as David continues to regularly post new images there.