I felt like it was pretty clearly indicated.
Somebody once caught the briefest of glimpses of a Zygon in its proper form. A child who hadn't learned to preserve its body print, who had been left alone to learn these things for itself. And then word went round these primitives that we were monsters.We want the truth of who we are to be acknowledged. We want to live as ourselves. At any cost. We want a home.
A human reacting with horror and fear to a alien child, that no human outside of U.N.I.T. and the Osgoods knows were placed within the general population, does not equate to the Zygons murdering the entire town (those dumpsters for off hair), and murdering members of U.N.I.T.
Also, Bonnie never stated she was doing this for Zygon children. Nor did she claim to represent the majority of Zygon views (like in a democracy). Bonnie had a grudge, and the means (superior alien technology and shape shifting) to strike back at the civilian population of Earth and the military who deals with aliens (U.N.I.T), and she took it.
I think a diplomatic solution could've settled this grievance before murder had been carried out. But like I said, I think Bonnie just wanted to start a fight. A fight she admits in "Inversion" that she knows she can't win.
I'm not defending Bonnie's actions-- I'm just pointing out that they're more complicated than EEEEEVIL, and that's why it's possible for her to be "rehabilitated" in the end.