LU: if I am not mistaken, it is the halachic norm to turn to a mumche in a particular issue to guide halachic decisions where the specific and current circumstances need halachic application. In this case, the mumche would be an expert in military discipline and Tohar haneshek. The IDF officer who wrote the policy would seem to be a mumche, and he came to a similar conclusion to what I wrote about this case, writing in an OP ED recently that this soldier did not act in accordance with Tohar Haneshek or his communicated orders.
Do you think that any army, let alone a Jewish one, can operate when each soldier makes all of their own decisions in a security situation? That would be incomprehensible to anyone who has served in any army or studied their actions. Each soldier does have the responsibility to question any order that violates the Tohar Haneshek policy. That is clear. But not killing the terrorist did not violate that policy.
As well, there is in application of Tohar Haneshek an active vs passive role. It is far clearer to demonstrate why one should save a life rather than why one should take one IN THESE circumstances (ie that the evil terrorist was already down, wounded and disarmed).
Israel and its army strive (sometimes, and fail, sometimes) to respect halacha; but it is not as currently constituted a halachic state as envisioned in the Torah (no melech, no kohen godol, no bais hamikdosh, and far, far removed from the agricultural society that most ste/land related halacha is predicated on). To thus expect its army to treat every enemy as Agag the Amaleki is unrealistic and frankly absurd.