The difference between that and the hypothetical Iraqis at JFK is that the Irish government would have to give permission for the troops to over-fly their territory. Unless Ireland has an agreement about this with the US, they have to ask the Irish foreign ministry for permission for each flight. Similarly, there is no controversy about their destination because the countries they are going to have agreed for them to be based there. If they were going to jump straight into Iraq the issue might be a little more controversial! I believe that shooting them down would legally be like sinking a merchant ship without warning, i.e. legally a no-no. But not that anyone cares about that since 1916. If they were actual military aircraft they would of course be fair game whatever. (although, are they like ships in neutral waters? Don't know enough international law.)