Others have made the point - and I've piggybacked off of them - that "She's Leaving Home" shows The Beatles to have been out of step with the counterculture of the late 1960s. The reasoning goes that, because John and Paul registered notes of sympathy for the parents of the runaway teen, they can't be seen as full-throated supporters of that period's youth movement. Adults - instinctively conservative and out-of-touch - were part of a system of oppression, and yet The Beatles, to a certain degree in this instance, sided with them. Some avatars of the youth culture!
Lately, I've been rethinking this idea from several different angles. First, it's probably unwise to infer a connection between the song's narrative and concurrent real-life events that weren't directly related to it. Yes, "She's Leaving Home" was based on a true story, and yes, John saw some of his life in it; but there's no evidence that The Beatles recorded this song as a means to comment on the burgeoning culture war. The story likely appealed to Paul because of the raw and complicated emotions involved. Then, to make the narrative more engaging, Paul and John let the parents have a voice. After all, they're songwriters, not social commentators; the main priority is an effective story.
Second, the lyric is indeed quite evenhanded, indicating sympathy for both the girl and her parents; but in no way does it fully exonerate Mom and Dad. Consider some of the lines that provide their perspective: "We gave her everything money could buy"; "How could she do this to me?"; "We didn't know it was wrong." They evidently thought that money and consumer goods could be a substitute for meaningful interaction, and earn their daughter's love. They were wrong, and The Beatles are saying they were wrong. With her remark, "How could she do this to me?," the mother selfishly focuses on her own emotions rather than her daughter's. Again, The Beatles are critical of this. John and Paul essentially depict the parents as misguided, emotionally clumsy, and blind to obvious truths. Mom and Dad had never truly connected with their daughter. Hence, "She's leaving home after living alone for so many years." That's the chorus - lyrically, the most important part of the song - and it's a strong statement of sympathy for the girl. Paul and John clearly understood her plight, and yet they were also mindful of the parents' pain. (How could they not be?) They considered both sides.
"She's Leaving Home" is a very human song, and I now think that connecting it with the youth revolt of the 1960s misses this critical point.