In my head I assumed that Sikozu had been captured, tortured, and had lost something of herself. While Scorpius does have his hatred of the Scarrans, I felt like his pre-emptive attack was in retaliation for something he wasn't willing to share with the peacekeepers. I felt like Sikozu's 'brainwashing' seemed to crack during her conversation with Aeryn. Sikozu was a recently turned spy and we just didn't get to see it happen, maybe.