Yes it is in the rules, but so is "Observing level crossings" and "Sticky Bidon" rules, but they are regularly flaunted, with no negative effect to the riders involved.
Interestingly, someone on twitter last night suggested that if Contador and Arun wanted to they could, effectively, overturn the penalty (I'll leave you to work out just how). I can't see it happening, but stranger things have happened.