CJ drama , Red mosque and all those troubles were created only to bring down the Mush's govt. Because he had mingled up with the country's mafia party MQM. MQM successfully exploited Mush on the instructions of their masters. This will always remain a problem with any Pakistani leader except for as IK said, unless there is a non-greedy leader "jis ka pait bhara hua ho". Only such leadership can keep a check on the rest of the corrupt officials. Otherwise these agencies will continue to exploit these greedy leaders and they will continue to be exploited.
well thats another side of the coin, but tell me, if only we had the right Justice system installed, the right leadership will be evolved and that leadership will stand against such expoiltation, no matter what ISI or entire establishment has to say or do, Justice Iftikhar is an example, he stood against the strongest dictator of all time and due to his few decision, public of Pakistan supported him, against the will of govt, against the will of ISI may be, all because he showed some character.
But when the govts of NS, BB used to be dissolved, people of pakistan (regardless their affiliation or loyalty to the parties) use to celebrate, even own if Most unpopular president of Pakistan dissolves the current govt. people will not come out on street as they have seen that Asif Zardari and his party lack the tendency to solve their problems.
This is where ISI or any agency ( internal or external) can intefere, so it all goes down to the characteristics of the leadership.