The other thing is, given how close this was to a station, I'm surprised someone just didn't say to heck with it and self evacuate. That has happened on Washington Metro numerous times - the train gets stuck somewhere for 2 or 3 hours, someone faints or has an anxiety attack, and they just pull the emergency exit and leave.
I hear Amtrak-lovers here saying they would not mind sitting in their comfortable roomettes and sleepers on a stationary train for 12 hours, but if it was me, after 3 or 4 hours, I would probably ask the conductor to let me off the train and walk 3 miles to the station, and since I know they would not allow this, the other option is to "call sick", then they would dispatch an ambulance or cop car something, I can get off the train, take first-aid for exhaustion etc and be on my way. Sitting 12 hours in an idle train is way beyond my tolerance level.
No, I don't think asking the conductor's permission is the right way to do it. He's just going to say no. If you're bailing, just take your bag and leave, not saying a word to anyone. Maybe tip the SCA to close the door behind you, if you're in a sleeper. What's the conductor going to do, if he even sees you leave the train? Run after you, tackle you, and drag you back on the train? Of course, now you're on foot, at night, in a place you don't know, next to a busy main line, but we're just talking ways and means, not whether leaving the train is a good idea.
Claiming to be sick wouldn't be a good idea, not only because it ties up medical resources, but also because you'd probably spend hours waiting to be treated at an emergency room. Having done both, I'd rather wait on a train than in an emergency room.