What the hell did Jefferson mean here on church and state?

[suigeneris]

I'm a Jefferson fan, my favorite freethinker, but hadn't stumbled on to this bit from his Second Inaugural address before:

"In matters of religion I have considered that its free exercise is placed by the Constitution independent of the powers of the General Government. I have therefore undertaken on no occasion to prescribe the religious exercises suited to it, but have left them, as the Constitution found them, under the direction and discipline of the church or state authorities acknowledged by the several religious societies."

The question is, how is this compatible with the wall of separation?: "I have ... left {religious exercises} ... under the direction ... of the church or state authorities..."

http://www.bartleby.com/124/pres17.html">Thomas Jefferson: Second Inaugural Address