Athena might be a good candidate. In all, most pantheons provide richer personalities than monotheism. Or we could pick a trickster god, like Coyote or Loke - since science has lots of gotchas and fool-ups.
Anyway, I cannot help but think of what might have happened if we had invented/found a deity of skepticism back there somewhere in the Middle East.
"Dear God, is the Earth flat?"
"Yeah shall find out for yeahself. I give yeah two hints: first find a harbour and watch the ships. Then go study numbers with the Greeks."