You can see the Red Squad cadet shivering in his boots in front of Leyton. They were forced to manipulate the network. They were convinced to do something good. In the end they would have supported Leyton's supposed military dictature. Sisko prevented that. They may have disregarded orders later on.
No surprise that Jake Sisko doesn't want to be "Starfleet".
I suspect throughout history esp. in war you'll find examples of people convinced they were doing good. But going back to "Paradise Lost" didn't he admit to commiting acts of treason against the UFP? So one could make an argument he clearly knew what he was doing was illegal and was under no obligation to carry out that order.