What I'm hearing is if the fare was free they'd have saved at least $104,000 not including the salary of public servants that would be saved instead of spent on the same fare.
That's not "all fares added up to 104 thousand", that's "the fares of people jumping turnstiles and walking in emergency exits added up to 104 thousand".
Keeping the status quo of not replacing turnstiles would have been cheaper. But making fares free would be more expensive.
Which isn't to say that it wouldn't be worth it. Public transit is hugely valuable due to the economies of agglomeration it enables and the infrastructure you don't have to build because of it. It benefits drivers, retail businesses, employers, etc.
An R160 subway car can hold 240 people; they run in 4 or 5 car sets. The E train has 15 trains per hour during peak times, and runs 10 car trains. So that's a capacity of ~36k people, and it shares tracks with some other lines at various points
A highway lane can support 2.2 k people per hour in free flowing traffic. That single subway line can move as many people as a 16 lane highway, assuming that there's no bottlenecks at the exits. Plus the cost of all the parking garages for 36k cars.