The argument against the existence of God can be adapted quite easily into an argument against consciousness. Both are mysterious, autonomous controlling forces managing hopelessly complex systems. In both cases, the behavior of the systems being controlled can be explained at any level of scale in terms of known, scientific principles. For example, the molecules in your eyelid react according to molecular distances and the energy states of their electron shells.
That's a crucial example because it illustrates the fact that you as a human being are a subset of the Universe. If I can use science to explain the behavior of the Universe to the point where I don't need God to interact with it, then I can most certainly explain the behavior of your body to the point where I don't need consciousness to manage it. That means that denying God instantly denies consciousness.
The argument in favor of God has some strengths that are not shared by the argument in favor of consciousness. For one, in the case of a human being, there is no instant of creation that holds any kind of mystery at all. An egg and sperm unite and we're done. Science currently holds that the Universe began in a moment of grand creation whose explanation baffles us. God, anyone?
The Second Law of Thermodynamics helps make St. Thomas Aquinas' case for the existence of God, but does nothing to help the case for consciousness. The Second Law tells us that we're heading towards an entropy death and there won't be any coming back from that. Time ends. St. Thomas Aquinas only needed time to be finite to prove God existed. Meanwhile, humans die when their molecular reactions no longer support the larger-scale biological functions, but time goes on regardless.
Another difference is that there are plenty of reliable people who claim they've had religious experiences, in some cases, miracles. I don't know of any who claim such instances were due to their consciousness, but not to God.
Finally, there is this. My position as a Catholic does not require me to claim that God is the controlling force in the Universe. That is the Muslim position. I do not believe that everything happens according to the Will of Allah. I believe that God created the Universe and interacts with us on occasion according to His own plan. That makes my proof of God much easier, but does nothing to improve the proof of consciousness. All I need is the Big Bang, the Second Law of Thermodynamics and claims of non-repeatable, non-measurable events to reach the agnostics' position. After that, I freely claim faith to get me the rest of the way. The atheists have no such support for their belief in consciousness.
So which side believes in the Easter Bunny now?
Exit question: Richard Dawkins, Christopher Hitchens and the rest are all smart people and in their conversations must have worked this out. They can't possibly believe everything they're saying because they clearly believe in consciousness. What's their game?