Hi there, Just saw your post. My maternal grandfather was Maguire from Donegal. I can assure you it is a Catholic name as is McGukin as far as I can tell (from Co. Tyrone, Northern Ireland)
The problem is sometimes Maguire was spelt in different way, in fact my grandfather had it as McGuire on his documentation. Also prior to 1922 before Republic was established records could have been held either side of the border (i.e. now Ireland or UK). Hope this helps.