I don't know your route, but if BART is the problem, skip BART, pedal across the Golden Gate Bridge and just ride the perimeter of SF. It's easily done, ping me if you need more info.
Regarding panniers vs. trailer: I recommend rear panniers plus a bar bag as they will limit the amount of stuff she'll bring. The most common first time bike tourist mistake is bringing too much stuff. When it comes to touring: less is more.
And as for mounting her panniers, look for a solution like this:
https://www.biketiresdirect.com/prod...-dlx-rear-rack This is the solution we're using on my wife's road bike this summer for a 60 day tour in Europe.
Whatever solution you choose, have several fully loaded practice rides before starting. Have fun and ride safe.