Disclaimer: The Melancholy of Haruhi Suzumiya is the property of someone whose name escapes me at the moment. Point being, if I owned it, I would not be wasting my time writing fanfiction for it.
Kyon, despite stating the contrary, did believe Haruhi to be God, or at least something close to it. Not that he would ever let Koizumi know; the guy's ego was already big enough. And he certainly wouldn't tell Haruhi, for fear that knowledge of her power would lead to imminent destruction of the world, something her ignorance of said power has ironically nearly caused on several occasions.
It wouldn't be too far of a stretch to say he had known what Haruhi was before any of the others had told him. He didn't know per se, but he did know something was different about her. It was a conclusion he came to the very first time he ever looked directly into Haruhi's eyes.
They say the eyes are the windows to the soul. Kyon was inclined to believe this statement. He has looked into many people's eyes, even his own in his reflection. He commonly sees normal things, which is to be expected from normal people. Some people's eyes shone with intelligence, some reflected the world around them, and some even had the dull glaze of stupidity one would expect from a fish.
In Asahina, he saw the subtle intelligence of someone who was aware of their actions and the consequences of those actions. This is unsurprising; being that Asahina is a time traveler, she couldn't be a moron if they expected the space-time continuum to survive.
In Koizumi, Kyon perceived the passionate heart of someone who is a borderline religious zealot. He truly believes Haruhi to be God, and only his common sense and self-preservation instincts have stopped him, and his organization, from flat out worshipping her. If they did, Haruhi would know doubt grow bored of them within the month, and suddenly they wouldn't exist.
In Nagato, Kyon saw many things. Cold, linear logic being one of the few things he could perceive in her eyes. Nagato is, pardon the pun, too alien for his comprehension. She is basically a computer, though it's quite a bit more complicated than that. Still, there were some human elements in her that he could sympathize with and understand.
The first time he looked into Haruhi's eyes, Kyon saw the universe. Plain and simple, he saw everything. It was so far beyond his comprehension, he needed Koizumi to point out what Haruhi truly was. Kyon tried to avoid her, frightened of this strange being that his instincts screamed at him about. Still, he found himself fascinated. He was drawn to her; drawn to the girls whose eyes contained the universe.
