The Edinburgh singer Jack Rutherford once told me that he had spent quite a lot of time and effort trying to trace a historical incident behind "Bonnie Susie Cleland" and came up with a complete blank. As far as he could tell, nothing like it ever happened.

The ballad suggests it was significant that Susie's intended was English. Not simply lower-class. Which fits with "8_Pints"'s suggestion.

Incidentally there's a beautiful tune "Born in St Johnstone and burn'd in Dundee" in the Blaikie Manuscript (on my website) which doesn't fit any version of this ballad I've seen - it needs shorter lines. So some significant alternative version has gone missing.