Maybe Greg or Jim could shed more light on the matter, but I was once told that within the lyrics there are two songs, both about Mary Hamiltons but the historical context is widely seperated.

'Mary Hamilton' which normally starts:
Oh word intae the kitchens come
And word intae the Hall
That Mary Hamilton's borne a child
Tae the highest Stuart of a'

Is about a lady in waiting at the Scottish Court of one of the James's (II or IV). In the version of this song that I know the Queen engineers Mary Hamilton's death for infanticide and the King offers her pardon which she refuses

'The Four Mary's' which normally starts with a chorus:
Yestreen the Queen had four Marys
The nicht she'll hae but three
There was Mary Beaton and Mary Seaton
And Mary Carmichael and thee'

Is about four Scottish noblewomen who attended the court of and were ladies in waiting to Catherine The Great of Russia. In this song the hapless Mary Hamilton is accused of theft and hung, the being sung from the perspective of Mary Hamilton's servant who must carry the tidings home.