The intent was to prohibit federal involvement.This church and state thing has been on my mind so here it is...
The intent behind it is to avoid religious persecution. It was written in a time that many people could look back a couple of generations at a time when the Roman Catholics or other churches with a lot of power were persecuting people who did not subscribe to their brand. It was a big reason for the influx of many colonists to this great nation.
(On a side tangent I'd like to add that if I were living in western Europe in those times I would also be a heretic, and subject to being persecuted based on my protestantism. So, in a way, my people have also been victims of the atrocities of Christianity, though you won't hear me bringing it up in a way to denigrate Catholicism.)
Now, atheists are bringing it up in a big way, why? Because our federal government endorses Christianity. No specific brand of it, but Christianity nonetheless. They don't go any further than the endorsement. They don't require you worship it, or that you follow a specific sect. But the intent behind the argument of separation is to weaken Christianity, thereby promoting their own religion, that there is no God. Which is an agenda that is religiously motivated.
Jefferson: "It must then be left to the states".