Maybe I'm being naive, but what's the big deal about standing up, facing the flag, and being silent for a minute or two while others recite the pledge?
I'm not particularly patriotic, but having kids stand and say the pledge wouldn't bother me as a parent or a student. I'm not religious, but I always had fun standing and reciting the lord's prayer in school when I was little, and everything wasn't so politically correct that teachers had to worry about everyone's sensibilities.
Kids shouldn't harass others in school about anything, so I think the usual school policies about harassment should apply.
You can't force them to do the pledge, but you can force them to stand and be silent, in deference to others. It doesn't hurt kids to be a little inconvenienced now and again.
I think you should address individual complaints as they arise, rather than worrying about them ahead of time. As a teacher, you must be used to complaining students and parents by now.
I'm probably not that helpful; mostly I'm just responding to support your implementing the pledge, if you and your district feel like it. I am so sick and tired of teachers having to be so absurdly p.c. that even having kids stand up silently for a minute has to have a whole policy written about it.
Here's what I *want* to say to complainers: "Stand up and shut up."
How's that for helpful?