The phrase "under God" shouldn't have been added to the Pledge of Allegiance in the first place. It favors Christianity over other religions.
For an individual who is an atheist, it is insulting to ask them to say the words "Under God" as they do not believe in the existence of a God-like figure. In addition, Jehovah's Witnesses though they do believe in a God do not believe in pledging to any symbol or object. Therefore, it is a violation of their religious freedom to force them to say those words.
It is not a violation of religious freedom to leave out "under God", because people can still choose to say the phrase if they prefer. As much as people have the right to express their religion by saying "under God" in the Pledge of Allegiance, they also have the right not to say it as well.