From Gaelic 'ail', rock or from the Norman French name Alan Alanus, brother of Galfridus Redberd was a witness in Perth in 1219.  Thomas Ailen lived in Jedburgh in 1641.  The Sutherland 'MacAllans', son of Allan are really Mackays.  The MacAllan is a patronymic so possibly the original Allan was a progenitor of the Mackay clan.