Well, I was all excited to be able to post some informed speculation, but it appears the story's somewhat out already. I worked in monorails very briefly a few summers ago, but they drill the ins and outs into your head pretty well, and I did well on my "test."
My initial thoughts were that this had to be some form of combination human/machine error, being that I've seen MAPO Red happen and it's not something you miss easily. It's sad to read the story and now see it may have been completely human error, and not that of the pilot (Something I assumed from the start as MAPO override requires consent of the central dispatch person [i'm like 90% sure on this, can anyone confirm?], who is supposed to be a supervisor of some sort.) The system is designed so that the driver cannot make an error like this. I'm still incredibly confused as to how this could have happened. There should have been at LEAST 4 people in the area that could have stopped this, even at 2 AM. Additionally, monorail pilots spend a minimum of 30 days working only the platform before they even get to do training to really drive the thing. These people know their surroundings.
Having the "pilot" in the monorail is what really makes the experience "magical" for Disney guests. If it pilots itself, it might as well be the tram at the airport. So what does Disney do now?
I, personally, think there's going to be some sort of mechanical failure here. It seems impossible for this to be 100% human error. Whether it was a MAPO failure, control failure (not braking correctly or being stuck in forward motion) it just doesn't seem possible for NO ONE to be able to hit an E-Stop button before this happened.
This is absolutely a tragedy in so many ways. As someone who's been behind that console in the past, it's chilling to see these pictures and hear this terrible news.