I generally support the right to protest, I don't have a problem with people that block a highway for a few minutes... but delaying mass transit by up to five hours? That's going overboard. If it happens again I would hope Amtrak police is ready to take them off the tracks.
Amtrak Police have only about 500 officers (most in the NEC) nationwide, and I think they'd be hard pressed to do any kind of massive crowd removal without the help of local law enforcement. UP Police aren't huge either, but the Bay Area is an important region for them. In this case local LE had its hands full. I'm not sure if neighboring cities could help since they rarely handle riots, although Alameda Sheriff could probably lend a hand. UC Police often renders aid to Berkeley, but they're probably on alert too at this time for the campus area.
From my understanding, the track blockers started leaving, but at a certain point the staff had to clock out by law and there was nobody to move the train.