Like you Allan I had always assumed that the last line of the 3rd. [4th.] verse meant being subjected to church discipline, having to sit on the cutty stool in full face of the congregation. Why would the session clerk be mentioned if this was not the case.
This line however gives us a clue as to the age of the song, as this form of discipline had fallen out of use prior to the end of the first quarter of the 19th.C..