So this is a load of crap, right? The Europeans don't seem to have problems boarding their trains, even at their busiest stations. One of the biggest attractions that Amtrak has is the avoidance of the security theater that airports are saddled with. Why bring something similar to your biggest stations? Are you trying to piss people off?
Your excuse that this is for security reasons is really stupid. Nothing is more safe than forcing everyone to stand in a tight mass in a confined concrete space. What's the worst that could happen? If someone really had nefarious intentions, and was for some reason intimidated by your "security," they could simply board at Newark, Back Bay, New Carrollton, or Alexandria instead. Your "measures" are rendered meaningless.
Quit the excuses, stop inconveniencing your passengers. Even the most loyal among us have their limits.