"The Vilna Gaon, who was a kabbalist, and who wrote extesivly on the subject does not see the so called problem you do." He did: see Aderet Eliyahu on Parachat Mishpatim, at the end. HaGra preferred Qabbalah to alien Greek philosophy, but that does not mean he was fond of the former... "For a simple explanation of why not, see his disciple`s book Nefesh Hachaim, which reconciles this issue simply enough that it can be taught to children." This is plainly wrong. Nefesh Hachaim was written in order to make a point of why Volohzin yeshiva's students would not study Qabbala. It does use the Qabbala rhetoric, but Rabbi Hayim himself was vehement against Qabbalah. Now everyone is free to speculate, isn't, that his real intent was different, that since nobody (except Jewboy of course) was clever enough to understand Qabbala, R. Hayyim preferred to prevent studying it, and so on. Leibowitz knew all this and much more...but this is besides the point.
Firebomb thrown during demonstration in northern Israeli town of Umm al Fahm (Haaretz)
from the article: 'Prof. Leibowitz, does man have a soul?'