For the 15 seconds that it takes for a class to recite the Pledge of Allegience, I think students who have a philosophical difference with it can do what many other students have done over the decades, simply stand there semi-quietly, shuffling their feet, gaze around the classroom in boredom at other students mumbling... whatever...
It may not be the most respectful behavior during the pledge, but I don't believe that this is 15 seconds of daily torture that is worthy of some BS ACLU lawsuit.
No doubt some "libertarians" on this forum will disagree with my perspective. But what the heck, they'd approve of pot-smoking drunken orgies with animals in the classroom as long as they didn't pay any school taxes.