They provided a cel phone repeater as an amenity/courtesy to their passengers. It's not part of their charter to provide cel service.
Their goal is to keep their passengers moving efficiently. By no longer providing that cel service, they disrupted the wannabe disrupters.
Their freedom of assembly wasn't interfered with, they just didn't help it.
If the protesters relied on cel phone coverage to perform their demonstration, then their strategy failed, and they'll have to come up with another way.
They increased the presence of police in the area, so the "how will I call for an ambulance" concern is a bit melodramatic; there were emergency personal already on scene, with non-cel communication capabilities.
Personally, I feel the right to assemble/demonstrate has been extended too far into the area of "I demand the right to fuck up everyone else's day", and applaud BART for doing something about it.