In this sort of situation could you not get the customer to sign a disclaimer saying you have explain the difference in tile size and how it will look but the customer has told/happy for you to continue?
Sorry to hear about your problem - personally I would go with graham31's suggestion and get a disclaimer form made up which the customer has to sign. It would at least give you some recall if the customer turns around later and says they are not happy with the look of the tiling.
I simply refuse to install, Politely of course, that way my reputation remains intact. Sometimes the smart thing to do is walk away when faced with problems that are out of your control, but if accepted then it becomes your problem and she is within her rights to complain (although not fair on the fixer) Yes she was warned and you have done everything right................ except you are the pro and you need to know what can and can't be done. It's not your job to try and make SH*T SHINE.
Rule of thumb if you dont think you can make a good enough job with the mats provided then dont do it once you fix them its on you.( it sucks i know but thats how it is )