Prior to the theory of evolution by natural selection, Intelligent Design was the theory supported by all the evidence. Scientists from Galen, Newton, Jefferson, Galileo, even Darwin when he was younger accepted this as the best explanation for how such amazing functional complexity could exist in the human body. The only alternative at the time being chance, and chance was a clear loser.
There wasn't a lack of any evidence, but rather a huge amount of evidence for the propositions. Which weren't as much magical thinking as we would think today as they were simply unknown. They weren't wrong for thinking this way. They honestly were very rational and went where the evidence lead them, and it lead them towards something that had many of the attributes one would ascribe to a God.
It actually was good evidence for God. Which is why when evolution came around and kicked that ideas' teeth in, all the foremost scientists in the world went from largely being deists and theists to being atheists. For this diversity of life to exist without God requires that there be a process like evolution that could create the diversity out of only randomness and time, and lo and behold there is *EXACTLY* such a process.
It isn't proof or certainty, but the fact of the matter is that evolution is good evidence that there is no God. It would be remarkably strange for God to create a universe whereby God need not exist, considering with God every universe would be possible. However, if there were no God, we would have to have a universe like this universe.
The chances that we'd have this universe are much higher if there is no God. And such claims that the only alternative to our current science is nothing at all is absurd. From preformation to Phlogiston and miasma, we've been wrong before, but we were lead there because that's actually what reasonable logical inference and evidence led us to conclude.
Ignoring such things and thinking the other side is a blank slate is actually kissing away an easy win. If you assert nothing, and they only assert bad arguments, when you've torn through their bad arguments you've finally managed to tie, because you never pointed out that what you're saying has always been the case and that the universe actually is particularly good evidence that they're wrong. And that what you're saying isn't an implicit assumption of science but rather the conclusion of science. It isn't that science must assume that the supernatural doesn't exist but rather than science works so damned well without it that that is considerable evidence that it doesn't. Science builds on the shoulders of other science, and the if one treats naturalism as a theory, you will find it has considerable evidence to support it, no evidence that contradicts it, and that it works effectively as a base theory for the rest of science. You need not exclude the supernatural a priori, you can do so a posterori. The supernatural doesn't work, it never has, and has always been wrong. It's not some special bias against supernatural claims but rather the fact that it's always been wrong that rightfully leads one to assume it would be wrong this time as well.