Accepting the reasonable assumption that Charles Fraser-Mackintosh was a reliable historian, and his articles does seem scholarly, it seems that there was definitely a senior MacGillivary called Donald killed just after the Battle of Culloden (16.4.1746). Leys is just S.E. of Inverness, approx half way between Culloden and Donald MacGillivary's home at Dalcrombie. It would appear that he was caught in the aftermath of the Battle and killed as he tried to reach familiar territory.

Whether this was the Donald MacGillivary of the song or not may now be impossible to establish. Much could depend on whether or not Hogg actually wrote the song or not and this may now be impossible to say with certainty. If he did, it's probable that the name is an imaginary one, a possibility suggested by Ewan MacColl, and asserted, without stated evidence, by Jack Campin above. If someone else wrote the song,a northerner for example, possibly associated with the MacGillivary sept, then it could indeed be about the specific Donald killed after Culloden.

I would like to think that it's the latter, tho I will always go with the evidence if it becomes available.