Difference is that CIA and Mossad served their countries well, regardless of what they did to other people in world. ISI, on the other hand, had some of its policies which turned out to be a national security threat to Pakistan itself. For example, creation and support of Taliban, IJI.
I think most of American thinks that CIA was involved in Assassination of Kennedy and they blame CIA as we blame ISI for creating mess at international and domestic level.
In case of Pakistan, where half of the leaders are corrupt and other half have openly admitted that Pakistan is a sin and/or mistake, ISI has to have its political wing and have to dilute the poison with poison.
I know ISI has been involved in forming and dissolving govts, but dont u think so it is because we have dumbest and/or opportunist leaders running the show, Only if these leaders had character, honesty and loyalty to the Country and been working for the people of Pakistan, ISI may have not involved domestically, but The purpose of formation of ISI is to protect Paksitan from both internal and foreign dangers, so they have to be involved in both fronts.