Of course morality stems from God (or rather, from an apprehension of a divine order, be it a God, multiple gods, a mechanism by which the universe works or something else along those lines).

The true atheist is essentially denying that the universe has meaning. By extension, any decision that any individual makes is completely arbitrary. Let's say you get one million people together and every single one says that murder is wrong. It's still arbitrary because the universe has no meaning. Someone could decide that all property is theft, and steal from others left and right, but believe that all murder (including abortion) is wrong. With no meaning to the universe, one can have a million moralities and no means by which any morality could be judged in any objective sense whatsoever.

The Greek sophistries that tried to say that immoral behavior would lead to a person being ostracized, or that pretending to be good while in fact being evil would still not work, have been proven false quite resoundingly by history. What contemporary consensus terms "immoral" tends to succeed quite well in many circumstances.

By contrast, if there is some meaning to the universe, then actions which lead to negative consequences are objectively bad, and so if certain behavior leads to suffering on the part of the person who commits such behavior (whether through divine punishment, the laws of karma, personal distancing from God, or otherwise) then that behavior is to be avoided. The universe itself provides an objective standard by its operation, much like the laws of physics do. "Thou shalt not kill" could be considered as logical as "Don't jump out that window - we're on the 75th floor".

The real problem that remains is determining just WHAT the universe's mechanics are. We all know that al Qaeda members think that God wants them to kill other people, and they expect they will be rewarded for doing so. Other people think that God does NOT want other people killed, and the al Qaeda people will be punished. Because we have no way of measuring if (or how) a terrorist, for example, was punished or rewarded in an afterlife (if such exists), it is impossible to objectively ascertain what is moral and what is immoral. However, if such an arbiter exists then such objectivity is possible (but outside our ability to know it).

How all this relates to Martin is that, if, for example, there is a Many-Faced God, then Arya's assassinations in his name might be rewarded, and as such they would constitute moral behavior. Sure, by most any rational standard which we would apply to the world we live in, assassination is generally bad, but the point is that we cannot apply real-world morality to a fake world unless we understand, metaphysically, how that world works.