I am not sure whether the burning of the church and its occupants in the 1600s would necessarily account for the absence of the surname Killoughy across Ireland. In general, people’s surnames didn’t come from the place they lived. Sometimes incoming settlers did name a place after their own surname. As an example, Irvinestown in Co. Fermanagh is named after the Irvine family who bought the town and surrounding area and then renamed it after themselves (as you do), but the rest of the occupants weren’t named Irvine. You’ll find people named Irvine all over Ireland, but they didn’t all come from Irvinestown. Indeed hardly any of them are likely to have come from there, save for descendants of that one family who bought the land.
According to this link, Killoughy is an ancient Irish place name going back to at least the 1100s, so not acquired by more recent incomers naming the place after themselves. I wouldn’t expect there to be any significant connection between the place name and the surname.
http://homepage.eircom.net/~killoughey/History.html
It doesn’t follow that people named Killoughy originated in that parish or county.
Looking at the 1901 census there are only 4 people named Killoughy in Ireland. All were born in Co. Westmeath. However if you search on Killough, you get 76, the majority of whom lived in Co Antrim. No doubt there are other similar spelling variations. Griffiths Valuation for 1854 has 7 Killoughy households, again all in Westmeath. There’s about 15 named Killough, in Co. Antrim and Co. Derry. Neither name is all that common. So one possibility to consider is that the spelling of your family’s surname has got changed over the years, and may have been slightly different in Ireland. If you know that your Killoughy ancestors lived in Tubberclare, I'd be inclined to focus on that area, and to consider possible alternative spelling sof the name thereabouts too.