Your concern is appreciated. Commonwealth was never against Gen. Mush or his dictatorship. He has been ruling Pak single handedly from few years with out any external pressure. Commonwealth is worried about the emergency imposed in the whole country and the reasons behind it.
Normally, emergency is imposed when a section of people in a region are unhappy with the govt and are taking law and order into their hands. But in this case it is clearly visible that anti-Mush segment is getting stronger by the day and it is unfair to back Mush against the wish of majority of people who are unhappy with his administration. And in such a situation it does not make any sense for commonwealth to support Pakistan since it has to do the same through Pak Govt ie Musharraf.
Having said that I do share your concerns regarding the common people who are getting deprived of what they deserve.