Thanks for the story-it reminds me of the same trip I have made twice to Athy. I, too, have had no luck finding my ancestors' graves there (1850's) even though a 1970's transcription says they are there. Perhaps the stones are worn away, like you say. I talked to the groundskeeper, Paddy Rice, about whether or not there was a plot of the graves, and unfortunately there is not-and he's too busy with local politics as the local Sinn Fein man to make one. Did you happen to see the broken stone with the tree growing around it near the ruins of the church? That was an eery sight.
I think to only way to find our ancestors is to access the grave transcriptions and find out who the "neighbors" are. I'd like to leave a new stone there, if I can find it, saying thanks from their decendants in America.
There people there were really great. We were even able to find Kirwan's Lane, although no one know which Kirwan it was named for. And if you go back, I recommend staying at the Pill Lodge-the best farm B&B around, just east of town.