Ballina-Cork via Athlone, Athenry and Linerick "works", but there are 2 reversals/runarounds necessary (Athlone and Limerick). Via Athlone and Portarlington there is only one reversal (at Port). Both routes involve single lines which are congested in daytime (Limerick to L Junction and Athlone to Portarlington).
The route via Limerick may also have a problem with some short passing loops, as freight trains would have at least 18 40-foot container flats. The main Dublin-Cork route is not congested south of Portlaoise: again one might need somewhat longer loops for freight trains being overtaken at Portlaoise, Ballybrophy, Thurles and Charleville. These would not be really major works: problably not much more than the cost of a printer in Leinster House for each loop.