The UCI rule book is almost deliberately vague on a lot of these things to give the directeur latitude and cover for these decisions... But ultimately neutralising / cutting short stages has precident and is just the reality of what is an extreme sporting event. There was a similar incident when Quintana won the Giro a few years ago.
The riders can quibble, but they were asking for some protection just days before.. and ultimately Prodhomme (sp?) Had very little time to make a call.
There must be more to life than football?
Neutralising stages does have the precedent, and by neutralising it returns the stage to the state at the start really. For example Cadel Evans' puncture incident, or the Milan San Remo where they upped and moved the race. I don't recall seeing a stage be stopped and times still be awarded, which for me is against precedent. Especially to pick a point in the race prior to the decision to stop it.