I agree that this a violation of freedom, but this is a case of religion being subverted for political reasons, not a problem with the religion. Almost every religious group has had its fanatics at one time or another.
Religion is a political subversion.
The Quran, in isolation, is not a religion. Same goes for the Sunnah, or the Bible, or other "primary sources." Human language is not a programming language, where one word corresponds to one action. No text of sufficient complexity can be understood in a uniform, objective, everyone-sees-the-same-thing way. Same goes double if the text is ancient, translated, or literary.
Instead, there are many interpreters--scholars, imams, clerics--who stand in the way and impose their own views, knowingly or unknowingly, on the original texts. Their own views create a new version of the text in their minds and the minds of those who listen to or read them. Simply by citing a certain passage and omitting a less compelling passage, they are creating a new narrative with its own strengths and foibles. Each narrative is built upon previous narratives (it is difficult to read one of these holy books in isolation without somehow being exposed to other believers, teachers, footnotes/annotations, or the media). Despite the differences (minute or extreme) between narratives, each narrative shares a lot in common with one another.
As opposed to an individual's narrative, the religion can be found in the complex web of relationships between books, theories, and people. Just like no one computer comprises the Internet, the entire network of relationships makes up the religion (and the Internet). And that complex web--the religion--is also a web of political relationships. Those politics are replete with broken promises, exaggerated fears, and insipid bullying--human problems from human politics. It's impossible to exonerate one's own narrative from the sticky web of human politics. You can't stand on the sidelines, because you're in it, no matter how badly you distance yourself from the ugly politics of it all.
Those fanatics you mention can't be so easily dismissed when they live in your web. Humanist Christians and liberal Muslims, take note: you need to own up to and speak out against your most destructive members. Especially when those members rule countries, lead political parties, and fund extreme acts of violence.
