That's a bit of an odd retort.
I think he meant we don't know 100% that God (doesn't) exists. Or, technically, 100% of anything. We can't even say with 100% certainty that we will die, as there is a tiny chance I'm immortal. Etc. I imagined it was more of a philosophical statement than a scientific one.
It was, completely down to watching "The Cell" on BBC4 the other night. My point is that, to me, with science being so advanced and the proof for evolution so strong, it seems more logical to believe in God not existing rather than being agnostic.