In a place like Afghanistan, I don't think it's possible to completely separate CT and COIN - maybe it is in the western world, but the line is practically indistinguishable there. CT is really an intelligence-driven enterprise - the difficulty isn't killing/capturing/disrupting terrorists and their networks, it's discovering and unraveling those networks and for that good intelligence, usually HUMINT, is required. Favoring CT in Afghanistan at the expense of other efforts like COIN would hurt that intelligence effort, IMO and thereby hurt the CT effort. Few are going to risk their heads (literally) to provide information to US CT forces unless there is some significant benefit for them.