There can't be free-will if there wasn't any choice. If there there are choices, there is the potential for evil choices.
So it's kinda like saying "if God is all powerful could He create a mountain on Earth but also make it so the Earth is a perfect sphere?" It's just pointing out that a planet that's a perfect sphere wouldn't have mountains and a planet with mountains are not perfect spheres. Which isn't exactly deep philosophical thought that needs a flow chart.
Also if proving something about religion is paradoxical proves that religion is wrong, by the same logic proving something about math or science is paradoxical proves those are wrong. Halting Problem? Math is false! Schrodinger's Cat? Physics is false!
But outside atheist dogma, most people accept there are things about the universe that are paradoxical. The Halting Problem doesn't mean we should discard mathematics, Schrodinger's Cat doesn't mean we discard Physics. Following this trend means that all of the efforts by atheists to point out paradoxes in religion doesn't accomplish anything.