There are two interpretations of that statement. 1. Judgement will begin by first "judging" those in charge of the houses of worship. 2. Judgement will begin by those in charge of the houses of worship judging others.
Either way is fallacious. These "words of God" as written by man are designed to cause fear and guilt, and are designed solely for the purpose of control over the masses.
I find it quite disturbing that rational and supposedly sane people are so enthralled with their indoctrination process as children that they truly believe these 'holy scriptures' to be valid at all, especially when there is no concrete evidence that they are based on any type of reality at all.