While a protocol would be could to codify, I think it will be too hard for those involved to really account for every situation. I guess there are a lot of ways it could take shape, more than just a "x temperature and y percipitation means..."
I think the best solution is to start with a scale of varrying implications.
Green-good to go
Yellow- Be careful but your well being is still yours/teams responsibility.
Orange- Be careful, stage still on, but no cut off and no limits on car feeding/bottles/clothes, (other rule changes I'm missing)
Red- Neutralized stage, everyone behind the Commissaire.
Black- Stage cancelled.
Obviously, it is pretty much what is in place now. So the important part is choosing who decides, and when.
As it stands, the parties concerned are riders/teams, organizers, UCI officials, (fans, and journos too, but won't have any input,)
One option is for a jury to be defined (one of each? teams rep., organizer rep, and UCI doc? Chief Comm.?), and then vote on the label for the day, each day. Rules with that label is binding for the stage.
As it stands, the gentleman's agreements are not satisfying the situation. While it won't make anyone happy, a procedure will at least leave people unhappy in the right way.