Their chief concern was the practice that existed in England, where there is an official church that's an organ of the state. That's what establishment means in that context. Under that view of the word, you can't very well establish something (that is, invest it with government power) unless it's organized.
You give them too little credit. While they were certainly informed by their own view of the world, they were trying to write a Constitution of universal principles. Read the ratifying conventions discussions, and you'll see talk about a lot more than setting up a "national religion."
You interpretation isn't supported by their words. In fact, it twists them.