I don't see Al Jazeera as either controversial or sensationalist. They merely have different filters than American news outlets, which are notoriously sheepish about showing violence in war coverage. Implying they have ties to terrorists because they get scoops from them is over the top. The news directors at the BBC or CNN would love the sort of "relationship" Al Jazeera has with various factions in the region.

I'm not sure what your point is about Al Jazeera contradicting the Qatari gov't. Are you saying you are surprised they can or are you saying you are surprised they do because you think news organizations should support the policies of their home gov't?