Peer review is also a flawed process, serving mainly to suppress legitimate research, while it does actually prevent some crackpot pseudo-science from publication. Most scientific innovation takes place in spite of, not because of the peer review process.
New science is developed through the process of heresy. Heresy is the specific target of peer review. But according to myself and Stephen David Ross in Metaphysical Aporia and Philosophical Heresy,
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If our convictions are strong, it is because science, art and politics are able to transform themselves through heresy. In the case of art, heresy includes the return to superseded forms. When variation and novelty themselves become the orthodox, heresy requires older orthodoxies. The heretical side of reason disrupts even the norm of heresy. It follows that reason is as deeply manifested in conflict as in agreement. It demands heresy as well as consensus, demands that every rule be challenged, including the rule of heresy.
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Peer review, for the very purpose of squashing heresy, keeps heresy honest and so functions as its own kind of heresy: one that should be scanned with a jaundiced eye and analyzed for agenda-driven behavior.
The idea of Godless science is one that Newton would have roundly and not politely scorned!