The problems of the religious no one seems to associate with the problem of Torah shelo Lishma (--Torah not for its own sake, but rather for the sake of power or a shiduch or money).
The Ari means to say that the Talmud is mixed with good and evil like the tree of knowledge of good and evil was. See the Introduction of the Eitz Chaim. R. Zeira came to Israel and fasted forty days in order to forget the Babylonian Talmud and to start learning the Talmud Yerushalmi.
The reason is there is an aspect of holiness and entry into holiness in Gemara. Like the Gemara says about one who has Torah but not Fear of God: "Woe to him who has the door but not the house." It is a door for holiness if learned for its own sake. But when learned or taught for money, it changes its character into something negative.
When people see the general kinds of insanity and evil in the religious world, they almost never associate the problems with Torah not for its own sake,- but rather find flaws in the Torah itself.
But to me the answer seems to lay in the intention. סם חיים למימינים בה סם מוות למשמאילים בה
