Atheism and science have nothing to do with one another. There are atheists that dont know jack about science, and there are PhD's who go to church. So intellect, rationality, and science have no baring on faith.
There are a lot of atheists now who fall back on science, sure, but most of them dont understand science and those that do make irrational leaps in judgment, view and interpret the world through the prejudices of atheism, and take on faith much of what they dont understand.
An ancient atheist is no different than a modern one: They have no personal experience to give them reason to believe in a god.
Atheists then would rationalize the same way atheists now do.