As I watched 'Khuda Kay Liye', followed by many debates and dialogs with islamic scholars on the issues raised in the movie and the references of quran and hadith cited therein, all that left me as clear as I was. If, for a while, I set aside the 'Jihaad to make the world a Dar-ul-Islam' aspect of Islam and just concentrate on the issue of why there are so many issues and so much emphasis for 'living by the book', it melts down to a very different plane - it's in the human nature.
As a pop-theory, without any claims of originality, Islam suffers the same fate that christianity got through in middle ages and Hinduism in Vedic periods; i.e - absolute rule of a single class - clergy in this case. They interpreted and mutilated everything for their convenience, precisely as tricks of twisted minds but in disguise of speaking for God. I see a pattern in all three religions - first of all, the clergy created a language barrier through Sanskrit, Latin, and Arabic, which were not the lingua franca but became the language of God. The process and stages were different though, but the end-results were the same.
Thereafter, clergy had a free run to change or interpret the so-called God's words. After language, they began dictating what to study and how to live - curbing individual freedom because there are God Spoken rules for everything. If draw the parallels further, they began hideous targeting. Simply, oppressing the easiest target they could find or the one which could retaliate the least. All three commonly chose women. Apart from that, christianity burnt millions in the name of witch-craft and anti-christ, Islam attacked non-believers, and Hinduism fought with Buddhists and in the absence of any other obvious targets, segregated its own one-fourth.
In this sense, organized religion, or rather, institutionalized religion is no different from or better than fascism or communism. In essence, all are based on seeking absolute control. And that is why, religion is no matter of theology, mythology, or sociology. It has to be studied in the light of psychology, where human brain becomes its own worst enemy in a bid to seek absolute control over its own petty universe.