Cut marks are again the key clue. In the skull of the teenage, upper-class 14-15-year-old dubbed "Jane" by those who studied the remains, the evidence is grisly. Clearly, whoever was seeking nutriment from this skull did not know how to go about doing so; there were three axe-blows on the side of the head, and three more severe ones at the back on the cranium, before the skull was actually split; this was followed by the use of a crowbar to break the shattered skull open. There are also a number of lighter cut-marks, probably produced by a knife rather than an axe, which indicate prior or further attempts to deflesh the skull; it is these cut-marks which are most similar to those seen on Franklin remains. Collectively, they tell of the attempts of a person unacquainted with butchery to butcher a fellow human being.
Brains of other animals were eaten by English folk of the Jamestown era -- indeed, their overall diet back home would have had its share of organ meats, intestines, and other animal parts far less commonly eaten by humans today. So their desperation had, in a sense, a goal perhaps less grotesque to the Jamestown settlers than to us today.
There are a number of resources and news stories online today about this finding -- the Smithsonian's site has the best, including an article in Smithsonian Magazine, as well as this video with the lead investigators, which also shows the reconstructed head of "Jane." From the content of her teeth, she seems to have enjoyed a higher-protein diet, which makes it more likely that she was one of the upper classes and not a servant.
No one likes to imagine cannibalism. But no one should think that, in the worst of circumstances, people of any culture or nationality are immune to it.