You are being a great parent being concerned about your little one. Relax!!! First of all if you look at things through JW's eyes is your being on this website any worse than letting your child salute the flag or celebrate a holiday? If you were to exclude everything pagan in your life that would meant throwing out your wedding band, not saying the days of the week or months of the year as they are all named after pagan gods and many other things.
When I was fading and felt uncomfortable doing things that I thought were wrong I would wonder why it mattered. According to JWs I was going to be destroyed for not attending meetings, not going out in service etc. So what did another 'wrong' matter. One thing my therapist told me really helped. He said "Ask yourself what validity is there in what they are teaching you. What validity is there in what your believe? And what do you feel most comfortable with?"
I think at 5 years old you can tell the child that you understand and God understands and it's ok if he wants to salute the flag or color a pumpkin etc. It is very hard for a child that age to do something different from what the whole class is doing. I would be more concerned about him being affected socially and psychologically because he has to do something different from all his little friends. You might want to explain to the teacher where you are at and why the child might seem a little confused. If you don't continue to pound it in his head that these things are wrong and pagan he won't worry about it.
For many years I fretted about what my four, now adult children were doing in school when it came to the holidays etc. Now in retrospect it was no big deal. They ended up doing things like smoking, drinking and other things anyway. I really regret not letting them be a part of school and what their classmates were doing. My youngest son who just graduated went to the prom and looked so nice with his date. He didn't go out and get smashed afterwards. It blew my mind that I once thought something as innocent as going to the prom was considered "evil."
Best Wishes