Well, the fact remains that Islam needs to go through a reformation, followed by loss of influence on any secular matters at all. That is the natural path of progress for all religions, as it should be.
Reformation is needed to get rid of Islam's pathological need to control the lives of its members on secular matters. This is something that Christianity went through in the 16th century during Protestant reformations, which fragmented the Catholic church and eventually led to current situation where Christian churches really don't have much, if at all, relevance on secular matters. The only exception would be the right to perform weddings as a state-officiated institution; other than that, if you wish, you can entirely ignore the churches.
In an islamic country, if you're born a muslim, you're sort of stuck that way as long as Islamic law remains the supreme law of the land. This is something that needs to change if these countries are ever going to experience peaceful existence without multiple human rights violations.
And no, sharia doesn't gain GET OUT OF JAIL card from critique just because it's part of islamic culture. Wrong* things are wrong regardless of their supposed origin.
TL;DR - Like all religions, Islam will be a problem as long as it's allowed to dictate day-to-day life and legislation.
*Wrong is of course a definition, subject to ethics and morality used. To make sure that the definition of wrong used is as fair and balanced as possible, I propose we use my definitions which are obviously the best ones.