No. You should not be made to stand for the Pledge. I can’t imagine NOT standing, but forcing someone to is the opposite of what our freedoms mean.
I also don’t agree with removing the innocuous “prayer changes things” as it is not endorsing a specific religion, but freedom of speech is the right to not stand.
Make him stand, and recite the POA, except those portions he does not want to pledge. Atheist or not, he still better support the USA!!!