God never regarded free will murder as obedience. As always is the case with obedience, it was only obedience if God said to do it. I believe the proper way to phrase your question is "Why did God tell Israel to kill in the past but does not tell them to do so now?"
Maybe it doesn't seem so, but I have found that if you hope to get the right answers (especially pertaining to God), you have to ask the right questions. If you ask God, "Why did You murder people?", He cannot answer that question because He never murdered people (He did send judgment that ended in their deaths). But if you pose the question this way, He can answer it: "Why did You kill or send judgment on people in the past but don't do so now?"
Some people suffer loss, bereavement, all kinds of illnesses, then ask God, "Why did You do this to me?" or "Why did You let this happen to me?" They rarely get any answers (this is where a good bulk of the belief that 'we have to wait till eternity to get answers' comes from), because they are asking the wrong questions and because their sense of being more right than God (i.e. they are angry at God and don't want to hear what He has to say as in the case of Job) deafens them to hearing His answers. A couple that loses a child, for instance, may ask, "Why did God... Why didn't God..." They would get quicker and more satisfactory answers (instead of heart-breaking and confusing answers from friends) if they asked something like this instead: "What happened?" and "Why did this happen?" This also is true for "Why me" questions (rarely any answers for those) instead of "Why" questions which leave room for answers.
All the above is to say that you are more likely to get the right answer and even to figure out the answer on your own if you consolidate all you wrote above to this: "Why did God tell Israel to kill in the past but does not tell them to do so now?"