I wondered about this. The most prominent church in Dunkeld is (and would have been) the Cathedral.

I found this on the web:

http://www.heartlander.scotland.net/gallery/..%5Cdac%5Cbook_Story_15.htm

An earlier Bishop, James Bruss (Bruce), appointed to the See in 1441, was sadly troubled with the Struan cateran "Robert Reoch Macdonoquhv," who was a scourge to the church and caused "plunder the church lands of Little Dunkeld." It has been suggested that it might have been these godless invaders and not the law-abiding parishioners who are thus alluded to in the local rhyme so often quoted in derision—

I think that the idea of it being related to aftermath of the '45 fits... There's a verse that mentions Geordie and Charlie.

Anyone else have any ideas?

Cheers

Steven