I think you have a misconception of science. Scientific Inquiry is a process grounded in reason where by contributions of many we eliminate bias and come to a conclusion that is good enough for action. Though this, we accumulate and build upon concrete knowledge laid down by previous luminaries. Forward a hundred or so years and we have the modern world.
Science and Magic aren't opposed with each other. You can suppose if we discover the existence of magic today, it will be classified as a phenomena and studied.
As for your question, ten thousand years isn't that long and they'd be just as mentally capable as we are. They don't have the blessing of complex culture as we do, which will make teaching many concepts to near impossible, but given a generation or two, we can probably even absorb them into our society and no laymen would be able to tell the difference.