another way I heard the story was that the woman's family disapproved of the alliance, they were courting in the glen and when the man saw they'd been followed he though Molly has snitched on him. In his anger he struck her before he realised what he was doing.

Bunting (early 19th c. Irish collection) had a tune called "Molly Bheag Ó" which is described as also belonging to a Scottish song about an officer who accidentally kills his lover. That tune is rather like the tune of "Will ye go to Flanders, my Molly O", I think.

compare with this Irish song Maire Ní Mhaoileoin