An essential problem with many religions is that they perpetuate the myth that they are essential to peoples' morality, but they use people for (their) amoral ends. In the Judeo/Christian/Islamic religions, there is a strong but unwritten tenet that anything done in the name of their god is good. A related unwritten tenet is that believers need not feel any responsibility (or even judge) someone who is doing something evil in the name of their god. Presumably, the god will sort it all out in the afterlife and responsibility is not our concern in this life. These tenets allow all manner of havoc to be wrought through the unbridled power it gives the religion. This havoc can show up as subjugation of women, fabricated myths such as the recent one about the United States being founded as a Christian nation, religious-based quack "cures" for the "disease" of homosexuality, or terrorist attacks as part of a jihad.
I propose that we recognize religions as responsible entities and hold them accountable for the immoral actions they cause. Surely, if religious groups can band together to bring people "into the fold", they can also band together to take responsibility for their flock. If a group or an individual does something immoral or illegal in the name of their god, then that religion should be held accountable for compensation after a fair trial. Repayment of the retribution should be left completely in the hands of the religious leaders and/or hierarchy to handle in their own way so as to keep the sanctity of the religion. They might impose tax on all related churches, for example, or require disproportionate penance by the particular sect, church, or leader involved. They can presumably also make use of their power of prayer, magic, or influence with their god to help settle the score. With retribution paid, a religion proves its moral integrity. If a religion refuses to take this responsibility, it effectively brands itself as immoral and it should suffer the consequences of any other evil movement. To emphasize, the punishment should go to the religion and not directly to the believers in the religion.
With religions being held accountable for the actions of their believers, the world will begin to stamp out the evil that occurs in the name of religion. Under this plan, the brainwashed minions who will do anything for their god will no longer be assets to a religion. Instead, they will be recognized as the undesirable loose cannons that they truly are. The institutions that create them will undergo drastic change or die out as a result. This is the most effective way of shutting down the religious "schools" that pump out easily manipulated, believing idiots by the church-full. Without the institutions of indoctrination, groups like the Taliban and the religious right will die out over time. The bin Ladens and Pat Robertsons of the world would no longer be able do harm on a large scale and they would be more likely to be held responsible for their demagoguery. Religions that are truly responsible will be able to truthfully claim that they have something to do with morality. Then, we can then do away with the rest without regret.