in this case the fact of the matter is that members of the armed forces of one state deserted their post and went to fight for another sovereign. If members of the British Army had deserted their posts in Afghanistan, the UK or elsewhere to take up the fight against Gadaffi, how should they have been treated?
That is a very simplistic and disingenuous view that tries to establish equivalence between the sovereignty of the Irish Free State and that of the UK.
To analyse your example, compare how long Elizabeth II and her predecessors have been sovereign in the UK (centuries) to the age of the new Free State in 1939. Let's say 1922 to 1939 = a mere 17 years!!!
Maybe professional Irish soldiers who had done more than 17 years in 1939 had more loyalty to a King to which they had sworn an oath than a so called Free State and therefore had more cause to desert than most
