No. It would be like a scientist concluding that based on availible evidence, divine intervention is the only reasonable explanation for evolution. The problem is that not only are such claims based on no evidence, but they rely on circular logic; ie "The scriptures say that Jesus resurrected, therefore he must have since it is the most probable explanation based on them", when you say that there is this implicit implication that they are the most trustworthy source.

Your friend is right though, historians value verifiable evidence and naturalism while dismissing the supernatural. There are some who will entertain the possibility, and a great many historians do belong to one religion or another, but in terms of academic history, we look for the most rational explanation.

To bring this to my own field, I study Buddhist history and if I were to take the sutras as they are presented, the Buddha could fly and see the past and future and so could a whole ton of people, but see, I don't think he could. More likely, these were things attributed to spiritual masters in India at the time and claims were put on the Buddha to glorify him.

So, no. I do not, and nearly every respected historian does not, accept miracles or psychic powers as "history" as such. However, studying what effect the ideas of such occurrences had on people or how ideas of these phenomena had on people is very much within the bounds of history; for example "why was the resurection myth important to early Christians and from where did it develop?" Hope that helps.