I am wondering how something could be intelligent and yet have no consciousness. Anyway, if this presence were to represent a sort of God, I think that for many people a God without consciousness would not be appealing at all. The idea of God loving you and caring for you is gone, since It does not have the capacity to do either of those things. There would be no reason to worship this God or pray to it. You could sit and marvel and the wonder and mystery, but it still would not provide you with any sense of purpose. Throughout history religion has continued to shape its views based on scientific discoveries. Each time something new is learned, a new gap is filled. I think it's only a matter of time before this "God of the Gaps" is totally eliminated.
I would say that IBM's Watson (the Jeopardy!-playing AI) is intelligent, but lacks a consciousness. Heck, modern smartphones are somewhat intelligent these days!
I just mentioned it because I think it's an interesting topic. Personally, I believe in a God that is all loving. But don't you think that if we do eventually fill in those gaps, there will be nothing else for us to strive for? I believe that the gaps in our knowledge and understanding are what make us human and should humble us. I do hope that there will always, regardless of technological or scientific advances, be gaps that we will never quite understand.
I agree that things would get pretty boring if all gaps were filled and everything was known. My point was that your theory on dark matter is no different than any others throughout history that have attributed unknown phenomena to divine intervention.
And I'd say all of those should at least be pondered as possible signs of something greater.