One thing to consider is lubrication. Without lube, the vagina is more likely to be torn when having an object (such as a penis) forcefully put in and taken out. Vaginal lubrication is generally produced when one is aroused or stimulated pleasurably, so a person engaging in rough sex while aroused would likely produce more natural lube and thus have a lower chance to be damaged. Of course, the penis also causes the vagina to become lubricated simply through friction, so this is worthwhile to consider.
I think a doctor would be able to distinguish between the two more accurately by considering any secondary damage, such as bruises, signs of choking, bite marks or nail scratches, etc.
Ultimately, I think the biggest contributor to the determination is what the woman says, how she acts, etc. I can see situations in which the physical results of rough sex would be similar if not very much like those of a rape, and one person may say one thing when another says another thing. A physical exam cannot determine the intent, after all, and that’s a big key in such scenarios.