To commit such war crimes, the GTVA would have to rip apart BETAC. You don't understand. YOU JUST CAN'T KILL PEOPLE INDISCRIMINATELY. Hell, we're losing soldiers all the time to guerrilas disguised as civilians in Iraq. WE'RE NOT OPENING FIRE ON CIVILIANS AT RANDOM. In the GTVA, the officers responsible for atrocities like firing on civilian ships would be prosecuted for war crimes. If they didn't prosecute said officers a lot of people would be really pissed off at the GTVA government, and since the GTVA is (or part of it is) a democracy, the citizens would exact vengeance with their votes come election day (it doesn't take a sociologist to figure out that elected officials want to stay in office). The GTVA would care that EA science vessels modified to become warships were attacking their cruisers and convoy but they would be able to do **** all about it except impose a harsher peace treaty after the end of the EA war.
Sure, we shot up civilians during Vietnam. That was partly why the antiwar movement was so strong.