The perversion of doctrine you describe is not an end unto itself. It is merely a symptom of a larger thematic disorder. As I mentioned a few posts ago, the deviance is not singularly chained to broken religious thought (or, to your point, the inability to critically think). Human social mores -- things like culture; inferior economic status; familial tradition -- invariably play a substantial role in the germination and subsequent application of individual behavior.
The suicide bomber did not begin as a fanatical zealot. Nor did the hierophant begin as a heretical offshoot. They were individually trained, after being exposed to various intellectual poisons that impossibly vary from culture to culture.
Certainly, certain cultural systems have a higher probability of breeding maniacal thinkers. The elimination of religion - as an ideal - will not necessarily change the course of this fortune. On the contrary, vulnerability is often the primary catalyst for many schools of deviant thought. Destroying an institution that, for many, provides a healthy alternative to uncertainty and doubt seems counterintuitive to the base point of working to establish a positive psychological environment (one where critical learning can cultivate, for instance).
Until we can find a means to harmoniously negotiate the infinitesimal, varied differences that plateau certain cultures while marginalizing others, we will always have patterns of thought and behavior that seek cultural equilibrium by any means necessary.
Religion is not the problem. The problem might not have a solution.