One of the distinctions we've seen being pulled into the light with the politicisation of what used to be the opposition in Libya and Egypt is the difference between moderate Islamists and Salafis. Moderates, like the Muslim Brotherhood, are learning modern statecraft and politics and at least so far seem to have managed an acceptance of reasonable pluralism in society. This is no small accomplishment; it is relatively easy (actually still fairly hard) to build a movement that has a cohesive vision of society, enough so that they can enter power. It is much harder for such a movement, once in power, to keep their eyes on their goals without using the tools of the state to end other groups; accepting pluralism and conditioning pursuit of some of one's goals on popular acceptance while maintaining the upkeep and development of civilisation is quite hard.
By having power, the moderates in Libya and the Muslim Brotherhood in Egypt find themselves needing to respond to challenges by Salafis to rule-of-law and a pluralistic state. This is a situation that offers them opportunities for maturation that's so far rare in that part of the world, but more importantly, it sets precedent for a long overdue discussion within Islam for modernisation of Sharia. Some legal scholars (I provide an example of Wael Hallaq, whose works I strongly recommend to those interested in the topic) have been tackling this, but so far there has not been a comprehensive effort to do so in a deeply pluralistic society (Iran comes close, but it's neither pluralistic enough nor are its experiences, being Shia, necessarily relevant to most Muslim countries).
If Islam is to continue to guide legal and moral norms in Muslim countries, Sharia will need a better modernisation than that provided by Islamist movements (which are a modernist, rather than traditionalist as they claim, invention); if it is not, a set of processes possibly similar to those that dislodged christianity from state function in western states will have to occur. Either way, the conflicts now between secular, moderate pluralist muslim, and salafi interpretations (pardon me for lumping Salafi and other forms of islamist movements, some of which better deserve the name, together; the analysis doesn't change much if I expand the term) are useful for permitting a discourse that has so far been both muted on the practical level and left to obscurity in academic circles. The actions of the militants in Libya and Sinai make it a pressing practical problem and in doing so open the door for popular discussion on a regional scale.