A rabbi was telling a story about how his friend in the army was "forced" by his commander to shoot and kill captured enemy soldiers, who had completely surrendered, under a general "no prisoners" policy that the Commander had enacted. He did it. Halachically can one do this, and generally can one blindly follow his (possibly non religious and amoral) Commander in battle? Can a captured and defenseless POW be considered a rodef, even when incapable of chasing anything or anyone?

Although one must be moral everywhere, the halachot of war are often different from regular life, as outlined in the Rambam Hilchot Mlachim, and many books of military rabbis like Rav Shlomo Goren, Rav Avichai Ronsky, and others, and as is often seen in Tanach. Until you are in battle, it is totally unimaginable, and cannot be dealt with in the same way as during normal daily life. That's why the most moral and righteous King David and others in Tanach, sometimes do things during war which do not seem very nice but are necessary under the circumstances. In the Israeli army, if such an order was ever given it wasn't given by a local commander but by the highest ranks who understand best the military needs (BTW I've never heard of such an order, and from my experience, the opposite is the case, but even theoretically or perhaps in the early wars of Israel:), and it would only be as a necessary step to enable us to battle beneficially, and not risk our own Jewish lives. If there is a halachic problem in the IDF, it's in the exact opposite (!) direction, where sometimes the orders are to have mercy on the enemy (who also use their own civilians as human shields), more than is dictated by the Torah, sometimes even endangering the lives of our own soldiers.