It's strikes me as absurd that criminal charges are being brought against a pilot period, let alone for such nonsense.
If as stated, this pilot broke no civil air regulations but only violated a company procedure any disciplinary action involved should be exclusively between the pilot and the company. The CAA shouldn't even be involved and the prospect of a year in jail for the transgression of a company rule is rediculous, in my view.
Are you quite sure there is nothing more to this story than what has been published here?