There are many, many holed stones in Irish graveyards. Some are obviously Xtianised holed standing stones (see Layd http://www.megalithomania.com/show/site/1086/3359 ), but others do not seem to be (such as at Castledermot for instance http://www.megalithomania.com/show/site/101/1123 or Glencolmcille station 9 http://www.megalithomania.com/show/site/1207/3764 ). I personally would like to believe that this is just an echo of the pagan past.

Many tombs had holes through their doorstones* or had quarter circles knocked off a corner, presumably to act as a gateway between lives. I think that holed stones in churchyards are either earlier monuments from the site's pre-Xtian past or a folk memory preserved in later traditions.

In Ireland the holed stones do seem to be at places founded by early and well-known saints, so perhaps it was just part of the 'Saint Kit'. Holed stones have been used for marriages and healing (I know of one that still is used for healing) for a very long time. Perhaps a saint needed one to perform some healing miracles in a manner that the locals could understand.

*So many of these have been lost because it usually the door that gets removed for access. A lot of French, Russian and Indian dolmens have holes, some of the Russian ones still have bung-stones.