Coming late to this thread... just looks like over-reaction by the UAL FO, who would have known all about the Cessna if she'd been paying attention.
I fly the bayshore transition probably once a month on average. I've had an airliner call an RA concerning me once, I was doing exactly what the controller said and the other traffic was already past my trajectory. The captain sounded annoyed but didn't make a full-scale event out of it.
Usually they will give you another route if there is a heavy taking off on 28L/R, over midfield or out over the bay. A couple of times though I've had a heavy take off in front of me, obviously keep an eye on it and be prepared to get out of the way if needed, but so far it never has been.
Actually I flew that route a couple of hours after the incident (and didn't know about it yet). All I knew was that SFO tower wasn't taking transitions (no surprise now). So Norcal took me over 280 at 3500' instead.
No big deal. Hope it doesn't mess things up long term for the bayshore transition.
n5296s