The number of terrorists in an organization that are irreconcilable is generally smaller than you may think, and also we're using way too broad a designation of "terrorist organization" as compared to a nonstate military entity that may employ terror tactics. Al Shabab and Hamas are such entities, as were the IRA (as noted above)
As noted with the IRA, there were splinter groups that rejected the agreement, but they are marginalized on all sides, but the point is that while extremist organizations tend to attract people who buy into the ideology totally and who thus will accept only unconditional victory or death as peaceful outcomes, most of them are just trying to resolve a grievance they have or to achieve a desired goal. The use of terrorism comes only when these groups feel they have to act, but lack the capacity for conventional military or guerilla warfare
For the longest time, the Taliban knew they were winning, or at least gaining momentum, which is why they violated deals they entered into, since they did not give the Taliban what they wanted relative to what they understood their position to be. If they were indeed properly beaten militarily, or beaten in such a way that they still had some bargaining power but not enough, then they would be partners for negotiation, but while they have momentum (which according to a downturn in attack numbers, they are currently losing), they will not want to negotiate
The point of this overly-long rambling is that negotiation only works at the right balance of power. Just like how we refused to negotiate with Japan at the beginning of 1945 in World War II. The allies had the advantage so totally that there was nothing to be gained by not just finishing off Japan
Edit: also, why the hell would anyone sign a peace agreement that dictated their disarmament, unless the consequence for not signing was total annihilation? Your guns are your only bartering power, unless your negotiating partner can guarantee that they will be equitable to you once you disarm. That's why negotiation works better with, once again, the IRA in Britain, because the long history of rule of law in Britain meant that the IRA could disarm without fear that it would just turn into a full-on pogrom against them, or that the British would turn around and arrest every single one of them. Can Somalia or Afghanistan guarantee such things to Al Shabab or the Taliban? I certainly wouldn't trust Karzai as a negotiation partner, but then again i as an American don't trust him as an ally either
Monster Hunter: pissing me off since 2010.
