Agreed. That's why money for transit shouldn't be used to install fare gates to keep homeless people out of stations. It should be used to improve service and reliability.
Social disorder is the responsibility of the province and the City should continue to ask them to step up.
Putting up fare gates improve safety in the platforms and trains, reduce the area which the Transit Peace Officers have to patrol regularly and creates, at least some safe zones within the system.
You'll no longer have people using drugs inside the trains, which is a plus in itself, and really hard to enforce without fare gates. Because of how platforms are, especially the underground ones, they're not the safest place to be, if there's a chance of someone hiding in a corner, behind columns, staircases, etc., while the outside access areas are generally more open and easier to survey as you walk in... The advantages are several.
Also, imagine that you're a rider, get to the station and you see people outside of the paid zone that makes you weary, you ca stay inside while you call the police/security/peace officers, turn back a move one station, etc., all while safe inside the paid fare zone.
As for your concern regarding houseless people, those suffering from mental illness and addictions, and social disorder in general, I don't disagree that putting up fare gates and increased policing don't treat the real underlying issue, but they do treat the symptoms and make transit, and the city in general, safer for the vast majority of the population.
It is just like treating a cancer, if you like analogies: you undergo surgery and chemotherapy to get rid of the tumor, but those take much more effort and time to be effective in resolving the symptoms for good. In the meantime, you don't leave the patient suffering from the symptoms, and do everything in your power to keep him comfortable, until the disease is cured/controlled and he no longer needs to treat the symptoms superficially.