Kant is not saying what the a simple reading of this sentence suggests: that he has to ignore the facts because they make it hard to believe in God. The reasoning that Kant is referring to is not reasoning that tries to show the non-existence of God --he is referring to reasoning that tries to show the existence of God.As they say, read the whole thing.
In Kant's time, there was a common belief that reasoning could be used to prove all truths, including the existence of God. There were various "proofs" of the existence of God considered persuasive by influential thinkers. Although there were some who didn't buy any of the proofs that they had heard, it was widely believed that the question of God's existence could be settled, one way or another, by logical proof. Kant rejected this idea.
What Kant is saying in that quote is that since reason can never, even in principle, prove the existence of God we should give up the attempt and rely instead on "faith", by which he means another way of arriving at the knowledge of God.
More generally, Kant argued that we have different ways of arriving at different kinds of knowledge. There is no single faculty that is the ultimate source of all knowledge. This is in contrast to a very popular view in his day (associated with Descartes) that pure reason was the ultimate arbitrator of knowledge. In fact the title of the book that contains this out-of-context quote is "A Critique of Pure Reason"
Update: Doc made an update to correct for a mistake for a misreading. I don't think it makes a huge difference to his interpretation, though.