I am afraid I struggle with the 'use the name they used' rule as virtually all Irish were illiterate. Some modern Irish feel very strongly about using gaelic spelling for their family names, but the vast majority use anglicised spelling.
What I am concerned about it that by using multiple forms of gaelic spelling, it will make it harder to find profiles.
Take one of the most reviled Irish in history, Dermot MacMurrough. He appears as https://www.wikitree.com/wiki/MacMurrough-19 with MacMurchada as current last name. But if you search by MacMurchada on Wikitree, you won't find him. Then again, if you put his most common name "'Dermot MacMurrough" into Google, the wikitree profile does not turn up. But "Diarmut MacMurchada" does.
I worry at times about Wikitree becoming a bit too inward focused and how our results play in Google searches should be a key criteria if not in naming conventions, then at least in profile presentation.
I ask because I manage several pre-1700 Irish profiles. The benefit of them on WIkitree is the amount of correspondence I receive from people who have found the profiles and the collaborations that then emerge, But if people can't find the profiles in the first place, then the utility of Wikitree is reduced.
I offer no solutions, because every solution has consequences. But I do incline to using the most modern commonly used form of the name as the 'headline' name while ensuring profiles and search terms also recognise and pick up more ancient variations.