That second paragraph would seem to me to suggest that Thos. Jefferson saw the Constitution as protecting institutional Churches (The Danbury Baptis Association, in this case) from congressional interference in its internal affairs, rather than preventing individual citizens from acting according to religious principles when exercising the rights and duties of citizenship.
The crucial point is that in neither the letter to Ursuline Sisters nor in the letter to the Danbury Baptists is even the slightest intimation of hostility or even distance expressed by Jefferson.Indeed, the Danbury letter is in response to a gift from the Baptists to Jefferson of an enormous cheese which they made as a way of dramatizing their support for him.
Accordingly the “wall of separation” comment does not suggest any fear of the influence of the church on the state. Neither the Danbury nor the Ursuline Sisters case implied any threat of "an establishment of religion."