I think you may be confusing two different Inchiquins. Now Murrough O'Brien, (Murrough of the Burnings),1st Earl of Inchiquin did have a bit of an unpleasant reputation, siding with Cromwell in the complex wars of the 1640's, and sacked a lot of south-western towns. He ended his life in Rome fo many years, atoning for his atrocities.
I think Carolan's Lord Inchiquin would have been William O'Brien, the 2nd Earl of Inchiquin. He was a Protestant, and did fight on King William's side at the battle of the Boyne, but I dont think he was notoriously nasty in any particular way(or no more than anyone else in that violent era). There was another William O'Brien, the 3rd Earl of Inchiquin, but I think the dates suggest that the 2nd is your tune man.

Frankly, if Carolan didnt mind, why should you? Go ahead and play it, it's a great tune.