Hi Ros,
I have a similar situation in my own family tree, an uncommon surname in a village, evidence that just the one man with this surname came to the village in the early 1800s from another area of Mayo (from Schools Folklore Collection), where the surname is common, but family oral tradition suggests that the families (only two) with the surname in the village today aren't related (though I think this is more to do with my family not wanting to be related to the other family).
From Griffiths Valuation, by 1856, there were two Lallys (both Patrick) in the parish of Kilcolman (parish for Garryredmond and Caraun) one in Caraun and one in Garryredmond. You can search Griffiths Valuation yourself for free online, just google it, and there's threads about it in the Ireland resources section.
The fact that the name was uncommon in this parish might suggest that John and Patrick were related. What sort of relationship is there supposed to be between the two families? If they were brothers then maybe looking at the names of their children might signify something. There was a pretty common naming tradition whereby the eldest son was named for the paternal grandfather, second son for the maternal grandfather and third son for the father. There was a similar tradition for daughters. If eldest sons and eldest/second eldest daughters names match up it would be a good indicator.
If you're in Ireland, a sometimes helpful source for the origins of families in an area is the Schools Folklore Collection, on microfilm in Mayo Co. Library, you can read about the collection on that website, but it depends on the material each school collected. I'm guessing you've already done some research with the usual sources if you have the couples names including wives maiden names.
I don't know if I'm allowed mention other websites but mayo-ireland.ie has discussion boards for local towns/villages in Mayo, the discussion boards are used a lot by people researching their family trees and it's a good website for more specific family/area/genealogy queries. I think Ballindine, Claremorris, Irishtown and Ballyhaunis would be the nearest towns to your villages, so it might be worth a shot leaving messages there about the Lallys, or even finding older posts there about them.
Good luck!