Fact is, neither side is standing on the high-ground and both risk the WTO tossing out the direct loans given to Airbus as well as the indirect subsidies Boeing won from WA state to have the 7E7 designed and built in Everett.
The DoD's funding of Boeing is no different then the European national defense agencies funding of EADS, even if the scale is different.
Also, nothing in the current program prevents the US government from giving direct loans to Boeing like the Europeans do to Airbus. Boeing just chose the DoD route instead since the US government was not keen to subsidize Boeing Commercial directly, as it would have indirectly helped Boeing Military which would have hurt Lockheed-Martin's ability to compete in DoD contracts.