It seems to me that if there were an intelligent agent guiding evolution, it would be one whose activity was less predictable and less tractable to science than the other kinds of forces that science is pretty good at predicting and explaining. So, it seems to me to be sensible for science to go as far as it can analyzing and predicting discoveries without taking design into consideration. Only when these sorts of explanations run into trouble should science look for something else.
If I understand a particle, I know what the particle is going to do, always and everywhere. If I am dealing with an agent, there is some predictability, but such an agent is less predictable than a particle. It's not as if I can't make any predictions for form any expectations, I can. If I am playing chess with a world title contender, I have some idea of what they will do, but surely not a perfect idea, otherwise I would be as good as my opponent. So, if there is a God, I think we should expect science not to be able to bring it in until we had everything else understood. And, I suspect, that will be be awhile.