Human consciousness can be unusually distinct and still not require a god.
Speaking very generally . . . If you are going to understand atheists then you need to understand how we approach questions. What we are looking for is positive evidence for a positive claim. We don’t automatically fall back on “God did it” when we can’t immediately find an answer to something. Instead, we will say “I don’t know”. If you want to change the minds of atheists then you must understand this basic concept. Of course, it is entirely possible for an atheist to throw skepticism to the side and decide to believe in God without needing evidence, but that’s pretty rare.
I don’t know what you might have in mind with the expression “unusually distinct,” but in the sense I would use those words, it seems clear that it’s not. All sorts of animals appear to have internal cognitive processes. And there’s no evident reason why any of those cognitive processes would have needed any sort of supernatural origin, gods or otherwise.
Loving a god, from the point of view of someone who doesn’t believe, doesn’t quite work. But I certainly can heartily endorse the “love thy neighbor” bit, and yet I do not see why this notion of “command” is relevant. Surely if (as I agree) it is good to love one’s neighbor, it would still be good whether one were commanded to do it or commanded not to do it, so that the “command” is entirely irrelevant in moral terms. And that command concept, as I have pointed out, causes the extraordinary result that people who probably wouldn’t murder children on their own nonetheless will affirm that a command from a god renders this act right rather than wrong. That result, bound up as it is with the long and awful history of human suffering, should caution against the principle of command having any role in moral thinking.
I would think that the better course is to think of “love thy neighbor” as a sort of postulate or axiom of moral reasoning, just as one treats other notions the same. As moral values are not “facts” one cannot “demonstrate” them factually but one can, on the basis of human experience, arrive at certain core principles that seem to be sound. “It is good to avoid causing unnecessary suffering,” for example, is not the sort of statement the truth of which one can prove, but it is probably (in my opinion, certainly) a good moral postulate. And just as Euclidean geometry follows from a reasonable set of postulates, moral philosophy can proceed, grounded upon postulates drawn from human experience. As you say, it is necessary to use rational thought and the application of conscience in order to apply these principles.
Even Thomas needed evidence that everyone around him wasn’t crazy and believing an illusion; the history in and the historicity of the Bible is the evidence.