I was thinking that because just about the whole peloton crossed, the organizers wouldn't take anyone out.
(otherwise you're left with the front group and a bunch of 25ish riders that
didn't weren't able to cross... and which organizer wants Rast or Saramotins as winner?)
However, they did had another explanation (which - if true - I can find some level of understanding in):
They said that about 10m before the peloton wanted to cross the railway the bell started ringing.
You can't expect a peloton that is doing about 50K/h to completely go into the breaks on such a short distance. Since this extreme braking would cause bumping/falls which would probably cause the first riders to potentially being pushed onto the rails, making it even more dangerous (then intentionally crossing).
Only thing is.... I find it hard to believe the first piece:
If you look at the images, you can clearly see that the beams are already going down when Sky goes under/through them (Sky was at that point leading the peloton). So either the bell and the-beams-going-down happens extremely rapidly after each other in France or either the peloton took a long time over that 10m.
As said, if the situation is really as suggested above (the peloton being extremely close when bell rings), I do understand that the first guys aren't going to break... and - unfortunately- the riders following them (top-athletes in search of a great performance/victory) aren't going to let the guys who already passed the railway "escape" (I assume that in the middle of the heat, people aren't thinking clearly and just think "don't get dropped now").
However, I don't buy it here... I believe the peloton was far enough out to still - somewhat safely - break in time