If you (as a company) make the mistake of selling her the ticket and letting her on the train, despite a policy that you put in place allegedly out of a concern for the safety of minors, then let her get where she is going. To do otherwise is to threaten the safety of precisely the population you say you are trying to protect.
The Conductor could have stopped her on the platform if he was worried: instead, he let her settle into her seat, the train started rolling, and then he decided to ask her her age. Bit late (yeah, I know, maybe he didn't see her amongst the throngs boarding in Olympia). At that point, any real concern for safety dictates you get her to Portland (where she was being met at the train by adults, the parents of one of the other girls). With apologies to Letterman, this is another "stupid OBS trick." Put the wrong guy in a uniform, and he not only thinks he's God, but wants to prove it.
Further (and very much on a different-but-related topic), Amtrak's rule on this is unnecessarily restrictive. Most 15-year olds (and certainly as many 15 year old females as 20 year old males) are perfectly capable of traveling on their own on a train. Children take trains to school around the world (and in many places in the US). My first overnight solo trip on a train was when I was 10 (NY to Chicago), and by the time I was 14 I had made twenty or more, some in foreign countries: Canada and England). No, my parents were not irresponsible (or at least, they did not see themselves that way, and neither did / do I). They were very present, caring, and safety conscious, throughout my youth, to the point of actually moving to a statistically safe zip code before they had children.
Having a parent sign a release for a non-routine (intercity) trip seems reasonable enough, especially in a litigious society. But a silly rule will never be respected (think of pedestrian traffic lights on empty streets). Amtrak is asking for trouble on this one, and they are going to get it, as here. But defending court suits that should not have to happen, spurrious or not, is not a good use of her tax dollars, even if you win every one.
When the UM policy was updated a year or two ago (and age restrictions significantly raised), several of my friends groaned loudly and went back to putting their children on planes and buses, or to driving them. If we look at highway accident statistics, exactly how do we think that that has worked out for the safety of the children in question?
Finally, yet a third different-but-related topic, regarding the 3-hours-to-pick-up: the mother who had put the children on the train was at work, in a meeting with her cell phone off (understandable: my cell phone is off when I am in meetings, too). By the time she organized with the father to have the children picked up, 3 hours had elapsed. I don't find that surprising: once my kids are on the train, I figure they are safe. Silly me. Sigh.