Consider the distinction between repeatable events from unrepeatable events. Repeatable events includes events that have repeated or may be repeated at will (as in a laboratory) or may possibly repeat in the future. Unrepeatable events are events that are very unlikely to repeat or are impossible to repeat. It is said that science only studies repeatable events, and it can be argued that history is the study (science) of unrepeatable events – not that it excludes repeatable events but that it focuses on unrepeatable events.
“Nature” could be defined as the realm of repeatable events. Then natural science would be the study of nature or repeatable events. Those events that are unrepeatable would be left to historians but ignored by natural scientists. But could such scientists rightly study the past while ignoring unrepeatable events? Ignorance of unrepeatable events would be a limitation and a defect. We would not expect historians to ignore repeatable events, so why expect scientists to ignore unrepeatable events?
We may well expect events that only involve inanimate nature are repeatable in some way. But are all events with living beings repeatable? The position of naturalism says, Yes. But at some point we need to say, No, at least some living beings have free will (or whatever you want to call it) so that their actions may be unrepeatable, and thus beyond the purview of a science of repeatable events.
Knowledge of repeatable and unrepeatable events may need different methodologies to address both kinds of events but it could not ignore either kind without bias. We need both the study of history, with its unrepeatable events, and the study of science, and its repeatable events, as independent disciplines. The synthesis of science and history would require a different discipline, perhaps called “scihistory” or “histence”, that would balance the input of each discipline with the other.