At the end of "The Birthmark," Aylmer both succeeds and fails. He succeeds in that he finally rid his wife of her birthmark. He fails in that…she's dead. What went wrong?
If you've been paying attention to Hawthorne's moralizing throughout the course of the story, you should expect something along these lines. As we discuss in "Symbols, Imagery, Allegory," Georgiana's birthmark is no ordinary splotch. For one, it represents man's imperfections – the very imperfections that make her human. On top of that, we are told over and over again that the birthmark is deeply imbedded in her face. We can guess that, symbolically, this means that man's imperfections are deeply imbedded in his character. In short, the odds of removing such imperfections aren't looking too good.
Yet that's exactly what Aylmer does. By ridding Georgiana of her imperfection, however, he also rids her of her humanity. Once she is perfect, once she is no longer flawed, Georgiana can no longer live, because she is no longer a person. This brings us to…
Hawthorne's message is that being imperfect is just part of being human. If you're not flawed, you're not human anymore. This is the case with Georgiana, which is why her spirit goes up to heaven and leaves her body.
As we discuss in "In a Nutshell" and "Setting," Hawthorne's story is rooted in his own scientific times and the scientific times of the previous century. He's writing against the notion that, through scientific experiment, we can discover, know, and do just about anything. Instead, Hawthorne seems to be saying, science has its limitations. Aylmer can't discover everything about Nature; he has failed in the past and he will fail again with Georgiana. Nature creates; man can only deform or occasionally, if he's very lucky, mend. We also get the sense that there is a degree of truth simply beyond the realm of scientific inquiry – look to Aminadab's character for these hints of a greater, profounder, unscientific wisdom.
One of Hawthorne's pointier points at the end of "The Birthmark" is that Aylmer didn't recognize how lucky he was to have Georgiana, and that he is at fault for ruining everything. As Hawthorne says:
Had Aylmer reached a profounder wisdom, he need not thus have flung away the happiness which would have woven his mortal life of the selfsame texture with the celestial. The momentary circumstance was too strong for him; he failed to look beyond the shadowy scope of time, and, living once for all in eternity, to find the perfect future in the present. (91)
In other words, "Nice going, Aylmer. You messed up everything."