People generally just want to keep their Islamic identity. They aren't against "freedoms", they are fighting for them.
Now what kind of governments will develop? We don't know. Oppression of previously western-supported dictators is what pushed most to have extreme tough and sometimes irresponsible positions.
Now that they are free to participate in the political scene, they are feeling their way, still adapting to the new scene. They are forced to become politically correct and responsible, because when you are in government, you have a direct affect on the people that choose you or choose to refuse to support you.
When people work collectively in a society that has many lawyers and intellectuals (as opposed to places like Afghanistan, which was destroyed by continuous wars for over 3 decades), this can only lead to reasonable outcomes.
Places like Somalia and Afghanistan are essentially places in which people live in poverty, and where most people are uneducated and illiterate. This leads them to extremism, and certainly isn't a model that people would accept in places like Libya, where the leader of the transitional government is a lawyer and able to develop a system that is Islamic and that would guarantee freedoms, far from interpretations of individuals here or there.
When you hear people talking about a khilafa system. Its just talk. The reason is that theres simply no such thing as a khilafa system. "Khaleefah" historically was only a title, and even some accused of being non Muslims (like the Fatimid nation), used that title, while perceived by most as anti Islam!
So theres no such system, and if asked to apply it, no one would know how.
Legally speaking, the system of government in Islam is "Shoora" (which literally means consultation), and is basically consulting the people and letting them choose what they want. How is the consultation done? Thats open for discussion, and its precisely why I said after dictatorships people will have long debates when discussing the best model for this, and trying to look for a model/system that can't be easily hijacked by any group in particular, whether religious or even commercial (corporations).
This is especially important in places like Syria, in which theres some opposition groups now, that are basically acting like opposition, but work for Iranian intelligence agencies. The large number of sects and ethnicities, causes some to be loyal to foreign countries, which can be problematic. Just like what happened in Iraq, which was essential given to Iran as a gift by George Bush of the US.
So essentially people are trying to feel their way through, and figure out the best way to apply shoora principles. What helps is that in Islam theres no such thing as a theocracy, because theres no central religious authority that can claim absolute truth, so things are left to the people.
Also, I think codifying Islamic laws is essential, and would help create a civil society. Because most of "extremism" today, is basically based on individuals that claim that they know, without any legal background, and without knowing principles of applying laws in societies and end up with very shallow understandings, and without understanding how societies work. Thats why they feel that they have to force everything. I think having people participate in politics far from dictators will help in leading people to have responsible, more moderate understandings of things.