Man versus society conflicts can occasionally be tricky or confusing, but the important thing to remember is that man versus society can take different forms. For example, in a man versus society conflict, the protagonist or hero might go against the beliefs of a society or flout conventional wisdom, which would be more of an internal conflict. A man versus society conflict can also occur externally, if the protagonist actually battles against members of society, whether it be the government, factions, or the popular clique at school.
In Harry Potter and the Deathly Hallows, Rowling uses both kinds of man versus society conflicts.
Internal Man versus Society:
Harry rejects the offer of help from the Ministry of Magic and the Order of the Phoenix, knowing that he must strike out on his own with only Hermione and Ron to aid him in finding and destroying the horcruxes. He knows that Dumbledore wished him to keep the knowledge of the horcruxes a closely guarded secret and cannot afford any leaks in information to get back to Voldemort.
External Man versus Society:
Harry, Hermione and Ron face danger from the Death Eaters, especially after Voldemort's minions gain control of the Ministry. When the Golden Trio must concoct a plot to infiltrate the ministry to steal Umbridge's horcrux locket, they actively pit themselves against the Death Eater-controlled Ministry. The "Undesirable #1" posters hanging all over the minstry are a great example of exactly how much the Ministry of Magic has turned against Harry Potter.