I'll grant that faith in the supernatural--though not in a single deity--is ancient and enduring. But I don't see why that suggests any truth behind it. Maybe it's just a vestige of some primal impulse lying deep in our genes, like an aversion to snakes. Or maybe it serves, in some way, to promote the survival of the species. Maybe we just don't know.
You make the point that empiricists ultimately have to confront questions they can't answer about the ultimate source of everything. But don't believers face the same problem? Suppose God exists. Didn't anything exist before God? What caused him to come into being? Why did he come into being?
You say it's disturbing to think that what lies behind the universe is nothing. But if God lies behind the universe, isn't it equally disturbing to think that behind him lies nothing? The persistence of bottomless riddles is not unique to atheism.
But your argument about the impossibility of proving God's existence raises particular problems for Christians, I think. Other deists might think of God as indifferent to his creation and therefore deliberately elusive, making it impossible to know him except by a leap of faith. But for Christians, belief is not just a "supreme act of imagining." It's supposed to be a response to God's incarnation in the form of Jesus Christ. A handful of real men and women (so we are told) came to know God in the flesh and related their experience to others, which has come down to us in the New Testament. God didn't want us to rely on mere imagination: He wanted people to see him with their own eyes; he wanted to astonish them with such miracles that they could not possibly doubt him, except by deliberate perversity.
If that's the case, though, why did he limit the exposure to such a minuscule share of humanity? There is no reason in Christian doctrine that God's existence can't be proven empirically: He could prove it right now to everyone alive, starting with the readers of SLATE. If he loves us, wants us to know him, and feels obliged to punish us for disbelief, why does he insist on keeping such a distance that we are forced to rely on our imaginations instead of the senses he gave us? All the arguments about why we have to rely on faith instead of reason sound like efforts to explain God's perplexing absence from our material world, which is by far his most conspicuous trait.
A more plausible explanation, I think, is that he isn't here because he isn't anywhere.
I'll pass over the question of how a merciful God could inflict this presidential election on us.