We should also realize that when missions tasked to ISI are couched under the "national or strategic" interests, tactical level considerations are typically overlooked.Not only ISI, RAW, CIA, etc. these are all beasts. But as you pointed out, these agencies need proper oversight, and they need to be answerable. The problem I have is when a agency like ISI take orders which they clearly know are illegal, such as those from Bajwa, were clearly extra Judicial and massive human rights violations. To still go ahead with such orders rather than refusing to proceed under the relevant army acts which clearly point to such a situation where a superior gives illegal order and the subordinate refuses to obey.
Hopefully, the new COAS was an ISI Chief himself before being replaced with Faiz Hameed. I am sure he knows how to tackle the beast.
You have to put this in proper context. Why is it that you say "The problem I have is when a agency like ISI take orders which they clearly know are illegal...."?
Is it illegal because you are seeing Pakistanis like yourself being targeted? What about when ISI has operated against other secessionists including TTP/BLA and even MQM etc. in the past? They too were Pakistanis so how did we convince ISI officers/operators to go after them and why did we not talk about oversight then?
That we did not impose oversight on ISI when it was operating against AQ, TTP, BLA, MQM etc. eventually lead to the same tactics being applied when the next perceived threat to Pakistan's stability came.