That's not what I got from reading it.
My reading is that an accident that was most likely caused by a driver falling asleep resulted in cover-your-ass style changes that have little to no measurable effect on safety, but cause massive real problems with the system that negatively affect millions of riders. And beyond that, they're shuffling blame around and waving their hands to distract people from systemic problems.
I mean, if the delays are caused by slowing the trains down, they should say "we've slowed the trains down due to safety reasons, and that's why there are delays". Then people can either accept that and move on, or do actual studies into the problem to determine if their course of action is correct, and if the trade-offs made are worth it.
I don't think it's some big hush-hush conspiracy; it's just garden-variety corruption and a desire to avoid fixing root causes of problems because they're complex and expensive. Easier to just keep collecting that paycheck while using "overcrowding" as an excuse to get more public money diverted to your agency.