Killing him will only create a martyr. Holding him prisoner will
inspire his comrades to take hostages to demand his release.
Therefore, after much thought, I suggest we do neither.
Let the Special Forces, Seals or whatever, covertly capture him. Upon his capture, fly him to an undisclosed hospital and have surgeons quickly perform a complete sex change operation.
Then return her to Afghanistan to live as a woman under the Taliban.