Let me start by saying that I am a deist who does not believe in organized religion, and was not raised in a christian faith.

I have no issue with the idea of atheism, and I do not believe that you need a foundation in religious belief to be a moral person. However, I consider being clergy for a faith you do not believe in is hypocritical at best, and unfair to your parishioners. These "secret atheists" should resign, and should do so quietly. If they are in the clergy to help people, then they should pursue a career in social work.

As far as the comparison to coming out, it works in the sense that you were living a lie, and have stopped doing so. Where it breaks down is in the direct betrayal of your flock, especially if you preach a fundamentalist faith like the subject of that article. A closer analog would be confessing adultery to a longtime partner, especially one who you had put through the ringer for your perception of their infidelity. But instead of one person, you betrayed the entire congregation.

I also have a big problem with people forcing their religion on others, and that includes the absence of religion. Whether or not you believe in religion personally, faith can be a path to happiness and improved life for others.