What Gerson sees as the problem is the lack of a foundation for morality in atheism, not a necessity to prove of God's existence, which holds no interest for him.
British author G.K. Chesterton argued that every act of blasphemy is a kind of tribute to God, because it is based on belief. "If anyone doubts this," he wrote, "let him sit down seriously and try to think blasphemous thoughts about Thor."
By the evidence of the New York Times bestseller list, God has recently been bathed in such tributes. An irreverent trinity -- Christopher Hitchens, Sam Harris and Richard Dawkins -- has sold a lot of books accusing theism of fostering hatred, repressing sexuality and mutilating children (Hitchens doesn't approve of male circumcision). Every miracle is a fraud. Every mystic is a madman. And this atheism is presented as a war of liberation against centuries of spiritual tyranny.
Perhaps this is why the Holy Father emphasizes the tectonic plate division does not run between the monotheisms of Judeo-Christianity and Islam (though it will take a great deal of goodwill, charity, and infused grace for all of us to see eye-to-eye). Rather, it runs between the vacuous secularist-atheist neo-paganism that is still growing like a cancer and persons who take seriously the God Who Is.
So the dilemma is this: How do we choose between good and bad instincts? Theism, for several millennia, has given one answer: We should cultivate the better angels of our nature because the God we love and respect requires it. While many of us fall tragically short, the ideal remains.
Atheism provides no answer to this dilemma. It cannot reply: "Obey your evolutionary instincts" because those instincts are conflicted. "Respect your brain chemistry" or "follow your mental wiring" don't seem very compelling either. It would be perfectly rational for someone to respond: "To hell with my wiring and your socialization, I'm going to do whatever I please." C.S. Lewis put the argument this way: "When all that says 'it is good' has been debunked, what says 'I want' remains."