We shall have to admit out different moral priorities. I agree in that we pick and choose our battles and I really was offended with how the Equinox crew showed no conscience. It was like they were desensitized and that justified cruelty. People have turned the other cheek in times of war. Chosen to exploit other races and the majority justifies it or simply doesn't care enough. That doesn't mean every case needs to be confronted head on and Janeway felt personally affronted by a fellow Captain. Faced with one of his loyal henchmen and with time being against her and against her own crew, she didn't look the other way.