Valthaeris, there are times when orders can be questioned. If you think the order is illegal, you do notify your chain of command and (if necessary) your Commanding Officer's boss. But you still carry out the order.

If a soldier had the option to question and disobey an order, their would be chaos in the field. Imagine a sailor questioning his CO about the firing of a missile....
You might be on to something, if you had occasion to actually read what I wrote, to wit:

...in violation of either the Geneva Convention or the International Laws of Land Warfare.
If your first line supervisor orders you to line up ten EPWs against a wall and put two in the back of their heads, you tell the CO on the grounds that you think that may just not be kosher, and he says "Illegal order? Nah, fuck 'em!", you do not do it anyway. I am not sure what 'research' you found to substantiate that, though I am sure it is intriguing.

Soldiers do not have the 'option' to question orders. They are obligated to disobey orders that are in violation of either the Geneva Convention or the ILLW. To use your own example:

If a sailor disagrees with the firing of a missile against a predetermined target, that is a damn shame for the sailor. The target has already been approved and cleared by the chain of command who exercises command authority over that launch and an operational law specialist who is authorized to say "Yes, we can blow that building straight to hell" and has already determined the legality of such an action. At that point, disagreeing with the morality of such an order becomes an irrelevant sidenote. If it's a military target, it's a military target. Sometimes life is hard like that.