Courts extremism is one of the most overstated and misinformed beliefs there is; this was during 2006, when anti-Muslim sentiments and the war on terror were at their peak.This would have actually led to more separatism and possibly independence. PL kicked extremists out of Bosaso, there is no world in which an Islamist led government in the south is accepted.
I think having a Taiwan-like situation, where both Puntland and the ICU claimed to be the true Somalia, would have been the best outcome. We could have had decades of talks between the parties to synthesize a new state, while on the ground facilitating peace and restructuring.