You know this whole seperation of church and state thing is a crock. Firstly, it is taken out of context as Jefferson was referring to keeping the state from intefering with the people's freedom of religion.
Secondly, the federal government would never take it to the logical conclusion. If the church has no place in government then government should not take off for church holidays. They won't give up days off like that. Also anyone who makes a living from the church, ie pastors and church staff, could not pay taxes as that money would have come from the church and would have no place in government. They're not about to let tax money get away as they would have less to line their pockets with.
The conclusion is obvious. Seperation of church and state is only used to curtail the individual's rights. Or that's how it appears to someone who isn't on the government's payroll.