The only time the boss was truely evil was when they put Jessica in the trunk of a car. That was a bit over the limit. For the rest, the boss only attacked when the boss was attacked.
On SR 1, she (I say she, cos that is my char. Not in SR1 of course, but it will be extremely confusing otherwise. xD) only did what Julius told her to do. And then Julius basically got scared of his own creation and tried to kill her. In SR2, she just woke up and saved Johnny from death row. But Stillwater was so messed up as you see in the opening trailer when you leave the menu alone for a while, you see a vid how Maero just kills a civillian for a small time robbery, the ronin cutting someone's head off in public and of course the Samedi spreading their drugs. So couldn't get much worse then that. So the Saints do what they did before. They clean up the city to protect its people. Though it seems more that they did it because they wanted power. But don't it was Johnny's idea I think to actually take action. The boss just wanted a beer. xD Then Ultor attacked them when the Saints were pretty much done, so the Saints attack back.
In SRTT, the Saints were attacked by the Morningstar and Johnny was 'killed' so they took revenge. And at Johnny's memorial service, they were attacked by Killbane and the rest of the gangs, so they attacked them back. It's always been like that, really. So I don't think they're really evil. Just anti-heroes. But yes, all the killing made the boss kinda cold hearted, so in IV she was shown that there are other ways, especially by Asha in her nightmare where the Boss fights her evil self. So as said before, I am really curious about what will happen to the boss in SR V.