All religions being ISlam of CHristianity generate their extremists or fundamentalists as they are based on irrational beliefs. So to remove the consequences, the best, in my opinion, would be to remove the cause: religions.
Generally, extremists are exploited (instrumentalized if this is understandable in English) by leaders, with a political / national / individual agenda. The recent policies of the US has made it easy for fundamentalist leaders to build their hatred, and to attract not so bright people ready to go and commit terrorist acts.
I'm ready to believe Muslim fundamentalists are more a threat than CHristian fundamentalists for the time being, but, please try to get away from the propaganda you're fed with everyday. there are not hordes of Muslim fundamentalists ready to destroy and march on the US and the Western world globally. I live in a country, and especially in a city with many muslims, and most if not all of them only want to live a normal life and be respected for it.
Also about the bible, the koran and other old books, I believe strongly in freedom of speech, and the right of every citizen (even the president of the USA) to criticize every book.