I assume you are basing your conclusion on this phrase from the article you cite:
The words of this pledge never seem to resonate as much. Here we were waiting for the President of the United States to speak to us because the spike in anti-Muslim hate had so skyrocketed that he felt compelled to address the issue. I had to fight back tears as we got to the last line of the pledge: “one nation, indivisible, with liberty and justice for all.”
The article does not mention the omitted "under god", much less indicate that the omission was deliberate. Was it actually omitted, or did the author made a mistake? I can't find anything else on the web discussing this, but I didn't look all that hard.