"Allowing people to get on BART without paying" is probably San Francisco's least important problem, as compliance with BART fares is > 99% among BART riders, which puts it above the federal income tax (~85%) and far ahead of parking meters (< 50%). If you want to use armed police to end some policy of perceived subsidization then the people you want to taser are parking scofflaws.
Also FYI BART is not a city agency and it has its own police force.