The organisers and commissaires made the correct decision. Everyone on the race was at risk, not just riders. Interesting comment about abandoned riders. As the stage was nullified it technically did not happen but points scored were kept, not time bonuses. There is a case to allow DNF to restart, a tricky decision for the commissaires.
So far as the stage 2 sprint was concerned, NB closed Matthews down, stuck his elbow out to obstruct progress, everything about his actions in the last 100 metres was "irregular". Correct decision, but I wish people on TV would stop using the word "disqualified" (Eurosport!!). NB was relegated, in line with UCI rules, to last of the group he was in, which just happened to be the leading 3, as a gap of 1 second separated them from the bulk of the remaining peloton.
So NB is third, and fined 200 Swiss. At this point of the season had the commissaires not acted it may have been a signal for mayhem in sprints for a while, with a danger of someone getting badly hurt by the more "exotic" style sprinters. It's tricky enough as it is without antics as seen at the end of stage 2. NB knew exactly what he did, and all the protesting to media is just being a bit "French" in France.