The lines in parenthesis in Jurph's lyrics are of course not part of the original composition, and are added only when the song is sung by supporters of the IRA (who may also be supporters of Glasgow Celtic). Otherwise the song is pretty inoffensive to British people, and there really is no reason for Jurph to apologise to his English friends. The story of the song is one from the time of the Great Famine, and I don't think anybody will take offence at the assertion that this was a Bad Thing.
This song is often sung by Irish supporters at sporting occasions, including Rugby matches, probably because it's almost certainly the best-known traditional Irish song, along with Molly Malone. It was sung with great gusto during Munster's recent European Rugby Cup campaign, despite the inconvenient fact that Athenry is in the province of Connacht.
A recording of this song by Paddy Reilly became an enormous hit in Ireland during the 1980s. and a rather unfortunate dance remix became a hit in 1999.
As regards the origin of Athenry, it's from Béal Átha an Rí, which means the mouth of the ford of the king.