Change, exception, call it what you will. I'm sure they would have happily accommodated almost anything, if it were solely at their discretion. But these are government related immigration rules, and their ability to dock in certain ports will depend on them following these sort of rules. I can't imagine they would make a change or exception for anyone regarding passports, any more than they would make a change to food hygiene rules, or other policies imposed on them from outside.
I sincerely hope you get your passport in time! I missed a flight once, in my extreme youth, when I woke up the morning of my early AM flight and realized my passport was still in the bank safety deposit box, which was not accessible until after take off. Had to rebook. Passports suck. Why can't they just trust us?? 😉
--Julian