So, reading the story, the cholera didn't arrive with the lads, but they came down with it while working on the cut. (In the 19th century people didn't know that cholera was caused by dirty drinking water - it was thought to be transmitted by miasmic vapours). They were quarantined, and some obviously became frightened by the hostility shown to them; they tried to escape and were slaughtered.
For interest, here's a Ruddy from Inishowen, who probably looks much like the Duffy's Cut lads.