I wouldnt be suprised if the CSD informed the captain of the discrepancy and of his/her concern for contravening the OPS manual. This then puts any captain in an awkward position, as he should back his CSD, even though it is not a democracy! So going through his mind is 'what if this old/young trout throws me to the dogs when we get back?' And by all accounts, having already shown no common sense, the CSD will probably let you down, so why risk it for a biscuit?
What is interesting is there is the pilot on this website that follows the book to the comma, and those that are willing to take responsibility for unusual scenarios and make allowances. Provided these pilots are willing, if they end up in gaol, to say they did their level best and were pragmatic in their approach and that they used their discretion and judgement when making their decision then thats fine! But dont moan when the company cannot support you because the book says you messed up.
I come from the Al Haynes and Eric Moody school of flying and I bet 100% that I can guess what they would have done in this scenario!!
Lets not forget, common sense is not very common any more!