I still think there at least was a real Mr. Wilford at some point, and that's the guy some people met and the man whose voice Melanie used, spliced together from what sounded like old shareholder meetings. He probably started the original company (whatever kind of company it was before everything started), but by the time people started realizing the Earth was in trouble, he may not have been running day-to-day operations anymore. My guess is Melanie was always the brains behind the whole train project, and Mr. Wilford was the figure head at that point. Maybe he was involved only by being the trusted face behind the plan, raising money, but Melanie was always the one designing and building the thing.
I'm pretty sure at least some second class passengers bought tickets. They just didn't get the same accommodations, and some clearly have jobs of some sort on the train. They specifically referred to the original tribunal as "ticketed passengers" from first and second.
Lilah Sr. clearly knows her daughter is a sociopath, but doesn't care. She told that story about her poking out her dad's eye, and also some of her facial expressions when they were talking to her early in the episode clearly showed a contrast between how she sees LJ and how her husband sees LJ. She knows what LJ is. I'm not even sure she likes LJ, but that's her "bloodline" so she'll do whatever it takes to protect her. Dad, however, still seems to be at least somewhat delusional.
In regards to commuting her sentence, I definitely think it was partly the issue of what LJ knew, but also I think there was genuine fear that that commander guy (is he the police commander?) might try to oust her, based on the reports from that meeting he had with LJ's dad and a couple other first class passengers. So it was also placating whatever portion of first would raise a fuss. Though I feel like there could have been a middle ground that would accomplish both. I don't know if they have any cells besides that one we've seen, but she could have had a short "jail term" and then been confined to her quarters as "probation" for however many years, or something.