It is determined by kneeling. Male characters that kneel, get chopped. The option to kneel is determined by how rebellious or submissive you have been up to that point. There was a bug that was ignoring this choice, but I am 99% sure I got it fixed in 0.3.2. Hope that helps.
Ok, so the problem is not a bug but that it's not at all obvious which choice causes it. Because you can choose not to after kneeling. And in fact I didn't even get a choice to say yes.
Or... maybe the bug was that I was asked at all? Was I not supposed to be asked for consent that they just ignore anyway?