The idea of using orphaned girls into SWA agents would be a good idea not to be passed up on. In the worst case scenario that they should be shot at or killed by the bad guys, Rome can easily use it as propaganda and paint the Padanians as murderers and child killers.
There's also two other reasons: in Italy a large part of the population is strongly opposed to euthanasia (indeed, the word itself has mostly a negative connotation in Italian), and children are pretty much held as sacred. It is very possible the program started as a misguided attempt at saving girls who had nothing to live for and were already mutilated, and went well beyond what the Italian population would be willing to endorse.
There's a good reason why only girls are used: in Italy there are strong expectations about gender roles, and while things are changing girls would still be instinctively seen as harmless until they open fire while boys would be classified as a potential danger, if only out of recklessness and rowdyness. Also, little girls being gun-wielding assassins is just plain wrong, making them more feared and adding a small chance of the terrorists freezing up when faced with the SWA agents.
At one point we discover the American government is involved in the program. But why are they relying on the Italians in the first place? Experiments on children conducted on US soil would inevitably be exposed and open the US government to huge lawsuits. Italy on the other hand is an ally with a well-documented tendency for politicians involved in Government Conspiracy to not be held accountable for their actions.
" was the OP to Gunslinger Girl? Muzzle flash. Ziplines.