In the past I have instructed out of San Carlos for years, and flown that stretch countless times.
Common ATC clearance is to remain west of the 101 freeway with an altitude restriction. The GA aircraft had a Bravo clearance if he was in that area. The other route southbound would be to hug the coastline and dip below 700 feet (if my memory serves me right), but that is so far north of the airport that any airliners climbing out would not be a factor.
I usually tell my students that the safest place in busy airspace is directly over the airport as most planes are usually near the ground. I've flown directly over SFO a number of times to stay well away from arriving and departing traffic; just had to keep an eye on a go-around. Listening to ATC, having a mental picture of what is going on, and anticipating ahead of the aircraft sure helps, It is busy airspace, but the controllers are often reluctant to give a Bravo clearance if it is too crowded.
Good thing nothing happened and it can act as a reminder to GA pilots to be careful when in busy airspace.