I wouldn't say Kira is equally guilty as Prin. Prin was killing in cold blood purely out of revenge. The fact that he was surgical in his murders (Literally) wasn't about protecting innocents, it was about making himself feel justified.
Kira's entire culture was enslaved, and he was living comfortably on her world, passively benefiting from that enslavement. Kira did not hurt him out of malice, she hurt him because it was the most effective way to advance the cause of freeing her people. That was the necessity and reality of Kira's situation, Prin was just trying to make himself feel better, and clearly had no regret or remorse for the millions of people killed on Bajor, or the millions more who would have been killed if it hadn't been for people like Kira. If the Occupation had never ended, Prin would have still been on Bajor, with a comfortable job in the house of mass murderers while Kira processed ore.
I think part of Kira did feel bad, she wished she could have taken back Bajor without having to harm noncombatants, she wished the Occupation had never happened so she wouldn't have been in that position, but she did not feel remorse or personal regret because she knew soldiers have no choice but to do things that are in and of themselves evil to prevent greater evil from happening to your own people.