Wars are fought with the tools we have, not what we wish we had. The military isn't a police force - it's methods were always going to be 'brutal' though the dramatic decline in terrorism in Pakistan has shown that they were also very effective.
With respect to the 'proof' aspect, yes, evidence remains critical. Just because someone goes 'missing' isn't in itself 'evidence' that the military or ISI was involved, or for that matter whether local police was involved. There are tribal feuds, local enmities, kidnapping gangs, TTP extremists either recruiting or neutralizing those who they see as threats. Yes, people were also likely picked up by LEA's & military/intel agencies because of intelligence obtained on their activities, but I see very little 'proof' that can differentiate between what is what.