I think this will not affect negatively on the privacy of a common individual.
Since agencies will have concern with anti-terrorist activities only, they will not bother to listen to every single call made by general users. As a matter of fact some elite organisations already enjoying the intervention in public calls,emails since long without let you know that you are going through security filtration vice versa. A good step hope this will help counter the terrorism and eradicate this menace from Pakistan permanently. Aamin!