Xanatos is about to be released, so finally Owen broaches the topic of the gargoyles. It's interesting that they have waited this long, and to me, speaks to the fact that Xanatos doesn't like the idea of killing in cold blood and that Owen knows this.
Owen, interestingly, is the only one who does not seem to have any issues with this. There are, of course, many villains in this series, and it is very interesting to me which ones would kill our heroes while vulnerable during the day and which ones would not.
Xanatos appears to consider it when he said he can't have them under foot, but I really don't think he has it in him to do it. I don't know if I think it's out of any particular nobility in the way we'll learn Macbeth has. For all he comes into this room saying he'll take care of the 'pests' which are obviously the gargoyles, he is less likely even than Xanatos I think to kill them in their stone states.
In that room, only Owen, if left to his own devices, would go to the measure without extreme duress. It's the practical solution, and he is nothing if not practical.
Honestly, I think Xanatos's reason has more to do with this idea that if he cannot best them himself in some way, then they deserve to keep fighting. I don't know if that's an honor thing or a weird dedication to some sort of fate. He is a mystical man in ways Owen Burnett specifically is not. He's sought out magic and the impossible against all rationalization, and his persistence and determination got him answers a normal person could never dream of. If the gargoyles, despite being alone and the last and outsiders and the outcast, persist on surviving and best all his attempts to get them to succumb, then who is he to intervene. For all he has reached a point where he is lord over his own life and come to wield power once not remotely imaginable for someone like him, that seems a power he does not wish to cross. Likely because it was that power that let him get where he is now.
It's just all very interesting. And yes we do, just after this, learn that this is Macbeth.