Sorry to be short, but then don't work through the meal period. If they refuse to pay you for it when they are legally required to, then don't work it. I know you have deadlines, etc., but bottom line, that is your supervisor's responsibility.
Or, at least, don't work with without your supervisor's prior authorization and make sure your time card is corrected.
Of course, all this is assuming you are a nonexempt employee.