This is an interesting question, and to answer it fully I think that you need to consider the fact that the novel was written by a white woman who was addressing the issue of slavery from the perspective of an outside observer. Stowe knew a great deal about slavery, and she wrote this piece as a serialized novel that was published in an anti-slavery newspaper. Her goal was to make the general public more aware of slavery and, while her writing style is uneven and she tends to over-romanticize her characters and storylines she does a good job of pointing out the immorality of slavery as an institution by making the public aware of just how bad conditions were for slaves.
Spiritually, the idea of imprisoning another human being (unless that individual was judged guilty of a crime) was not something that would be considered morally or spiritually acceptable. However, the popularized conception was that Negros were nothing more than animals; therefore, this mitigated any responsibility to treat them as "human beings" from a moral perspective. This stereotype was perpetuated in literary works as well as in general society to the point that many people agreed with it. In her journal, for example, Sarah Kemble Knight(1704) expressed surprise to see black people in New York eating at tables with their white masters noting that "into the dish goes the black hoof as freely as the white hand" and this sentiment was not uncommon. However, it can be viewed as morally and therefore spiritually damaging, from a religious perspective, to those who believe it. By crafting black characters who were human in all of their feelings, desires, needs and expressions of self, Stowe gave her readers black people with whom they could emphasize thereby seeing the error of society's ways. This empathy, as well, points to the fact that slavery can be viewed as emotionally damaging especially to those who knew that their actions were wrong.
As to physical damage, there are certainly instances in which slaves did harm to their masters, but this is less of a theme in the novel as the focus is more on the generating support for the abolitionist movement.