historians do often engage with counter-factual positions, though it is somewhat limited. This is particularly true in the study of patterns, where the idea is to examine how external factors or variables interrupted or altered the flow of events. Examining this can sometimes lead the historian down a short path where he/she reasons how events might have occurred had said events not taken place.

An example of this can be for instance - how might the relationship between Pompey and Caesar evolved had Julia not died?

The historian cannot however do much more than go down a very short path, making nothing more than general comments, because at the end of the day, none of this is verifiable. Since there are obviously no "sources" for events that might have happened, it is basically speculation, and so can't really be deemed more or less valid than any other form of speculation. Thus for example, were one scholar to argue that Pompey would have simply retired, he would have no real basis to dispute someone else's position that events would have proceeded as they did regardless.

You might also want to look into historical revisionism if you haven't already. We often receive somewhat contradictory stories about the past from our sources. Historians have been known to posit alternative explanations that contradict recorded narratives about the past. W. Heckel for example (though I got this second hand, and long ago, so I don't have direct references on hand) had proposed that the reason Alexander didn't proceed much beyond the Jaxartes and Hyphasis rivers was because of his own plans, as he was keen to only conquer the full extent of the old Persian empire, not more. This is in contradiction to most established narratives about the events. Now I'm not offering this up as being correct, merely saying that exploring an alternative form of explanation for why things happened comes close to the essence of alternate history at times.