This may be an unsatisfying answer, but the truth is that by and large, professional historians neither seek alternate explanations nor accept the religious explanations as factual. The approach taken by most is to treat it as a fact that this is what the objects of historical inquiry believed to be true, and explore the implications of that belief and the actions taken as a result of it, rather than try to determine the objective basis of the belief. For example, there are many reports of miraculous fasting among medieval Christians, in which an individual is said to have abstained from all food for months or years. Obviously this is not something most modern historians, if you pin them down, believe could have literally occurred. However, they also don’t tend to find it particularly interesting to try and expose a fraud and explain how the fasting story was maintained and who was complicit in the presumable lie. Instead, they are interested in that the story was told and believed, and what that says about how medieval people thought about food and the body and sanctity. It’s mostly impossible to, in a historically rigorous way, come up with a well sourced explanation of events about which your sources have their own explanation. And even if it were possible, it’s mostly not as interesting as taking beliefs seriously for the value they had to the people you’re studying.