Here's my new 'history' of our ballad. It seems that Queen Mary's chamblerlain, an Italian composer named David Rizzio, must certainly be the one who learned about the affair of the French woman named Mary Hamilton and the Lord Darley, the apothecary, and wrote a disguised account of it and extended the tale to its logical conclusion as "Mary Hamilton", and, of course, composed our beloved tune for it. To Darnley it wasn't well enough disguised, so taking slight umbrage at Rizzio he and friends subsequently murdered him. The English got a very much whitewashed version of the tale, because in the ballad of Lord Darly [Darnley], (ZN1112 in my broadside ballad index) we find:

There dwelt a stranger in the court,
Sinior Dauid calde by name,
He was the first that went about,
This treason vile to frame.

The English were never told what this treason vile was, but now we have cleverly deduced it. Darnley didn't outlive him by much, but he wasn't killed for infanticide as far as I have been able to discover

Plausibily can fill in most gaps in our histories quite well.