In regards to combat, what sorts of skills or abilities would this Natural Philosopher have? The thing about wizards is they study magic so that they can cast spells, and they only study magic because they can cast spells in the first place. Gaining knowledge and understanding about natural law doesn't directly help you unless you can develop methods or devices that incorporate that knowledge (technology). The thing technology has over magic is the user doesn't necessarily have to understand how something works in order to be able to use it. The same goes for many magical devices. Maybe if there were certain items that only the natural philosopher could use because they require extensive training and understanding, I could see it being a class.
Outside of combat, what would they be able to do better than a warrior, thief, or mage who is versed in the scientific method, other than being pretentious about it?