Separation of church ans state, but who is protected?

The state exists to protect its citizens. The principle of of the separation of church and state keeps church and state from having undue influence over each other but no one seems to care that under current SCOTUS doctrine, this principle does not protect the citizen from the church to which he belongs.

If a citizen/church member brings suit against his church for violation of his rights the current doctrine allows the church to argue that the court has no jurisdiction over the matter because it is a purely religious matter.