Can't help you with your specific family but I would confirm that it was very common for Presbyterians to be buried in Church of Ireland graveyards. This still happens to this day. A specific example being in Bellaghy, Co Derry where neither of the 2 Presbyterian churches there over the years ever had a graveyard and so the COI one has always been used. So you should check any COI graveyards in your area.
Though COI keep burial records (unlike most Presbyterians) they tend not to record any burials in their graveyards by other denominations. So no help there, I am afraid.