the catholic church suffered from the same problem as Islam, but for a different reason. the Catholic church perverted the teachings of new testament. one of the reasons they went after Martin Luther is because they knew that if the general population actually read the new testament the church would lose a lot of it's power. if people found out that you could have a relationship with God absent the church, the church figured they'd be in trouble. you can't follow the teachings of Christ and have things like the inquisition, confession, payment for salvation, saint worship, relic worship, etc. there was not much in the operation of the catholic church that was remotely Christian. to the extent that they have kept some of those old teachings they still are in direct opposition to biblical teachings.
on the other hand, if Muslims follow literally the teachings of the Koran and their other holy writings, they have permission for their radical behavior. this has been the pattern of Islam from it's inception. those Muslims who are not engaged in radical behavior have made a choice not to take some of the teachings of Islam literally. as the catholic church has set up to pope to be the voice for God on earth, so have the Muslims set up their leaders to be the interpreters of Allah's will on earth.
when questions about behavior are raised, as they were after 9/11, it's the leadership that issues a ruling. after 9/11 some Muslims were upset that civilians had been the target of attack and without warning. also that Muslims had been killed. a fatwa was issued by leaders who said that the attack was ok because of the greater goal. the fatwa went on to say that WMD are acceptable also even though the majority of the deaths would be to civilians. another more recent fatwa issued in Iran has give permission for nucs to be used.http://carnegieendowment.org/static/npp/fatwa.pdf
here is the WMD fatwa, although to be fair, the Saudi govt did force him to withdraw it later. however, if you read it, you see how he used their holy teachings to justify the actions.