Great article! The points made are indisputable. Of course, the rub is that years and years of off-peak delays, single-tracking, etc., is very bad for low-income workers, as well imagine the cumulative effect of many hours added to commute time.
So, as Ross mentioned, any future shutdowns need to have some sort of alternative service plan rather than leaving vulnerable riders to fend for themselves. But if shutdowns can get the system to something approaching a state of good repair faster, they need to be strongly considered. That way the next generation of riders won't have to suffer so much on a daily basis.