Earlier quoted context omitted.
Good news, the CoC is inclusive for you, with the following: "those who wish to participate" ... "are expected to conduct themselves in a manner that honors the overarching spirit of the rule, even if they disagree with specific details. Polite and professional discussion is always welcomed, from anyone ." In other words, calm down.
That's as much inclusiveness as "stop hitting yourself" is your friend's good advice. If the CoC started with "First of all, purge any God from your heart" you wouldn't have thought twice about condemning it. But no, the atheists should just suck it up.
I think the Golden Rule is a wonderful Code of Conduct and it's how I try to live my life. If only more people followed that rule.