What schools should do is take advantage of the harsh flu and increase the prize money for perfect attendance. Instead of a $50 gift card make it a $500 gift card. This will be possible to do because instead of ten or twenty kids winning the award, you'll only have one or two. Even if twenty students keep coming to class with the flu it won't be long before they start dropping like flies and only the strongest will be left standing.
A student and their family who is able to last the entire school year without contracting and spreading the flu this year deserves an appropriate reward rather than NONE. If you want to avoid sick kids coming in to maintain their perfect attendance just let it be known that if they're seen coming to school sick they'll be sent home and disqualified from the contest. It's as simple as that! By eliminating the perfect attendance award you have basically conceded defeat against the flu and assumed that everyone will get it. Well everyone won't and the one kid who doesn't deserves to be master of the school.