All it means in simple words is that before ISI (and its internal wing MQM) and IB were funtioning in conjuction with military services and reporting to CIA but now it will be functioning in conjection with the mininstry of interior for the purpose of sharing of much more confidential info under this ministry so that destablizing Pakistan is easier than ever before due to sharing of the confidential national info and resources.
** In other words, the terror parties (CIA, IB, MQM) within Pakistan will now have much more control than ever before in running the government of Pakistan. ** Dissolving of Mushy's govt. happened cz despite his incompetence, he still dared to reject commands of CIA which he thought did not suit national interests but Pakistan's new government has crossed all the boundaries of corruption. They'r following ISI (CIA's) every order tilting its tail like a loyal dog. Mushy was not that bad. That's why his govt had to be dissolved.
The terror party you mentioned, the MQM, was a part of Musharraf's Govt. They were like his loyal dogs, taking his orders, May 12th being a good example.