I don't have the references in front of me, but the young Sam Clemens was
certainly aware of problems with slavery. I forget the boy's name, but Sam
wrote he complained to his mother about a young slave singing and Clemens'
mother told him he shouldn't criticize--that the boy would never see his own
mother again and the singing was his way of expressing his pain. In his
Autobiography, Twain mentioned slaves he saw by the river in chains and the
impression this made on him.
I think the LOM reference was specifically saying Hannibal slaves weren't
mistreated in the sense of beatings, lynchings, or obvious physical
mistreatment. Throughout the South, slaves lived very different lives
depending on location--hence the phrase "sold down the river" which everyone
knew would be punishment for slaves as plantation existence was far harsher
than more domestic duties upriver. Both these situations are important in HF
and Puddn'head Wilson as well as Uncle Tom's Cabin.
If memory serves, I think Sam wrote somewhere that Hannibal citizens frowned
on poor treatment of slaves. I don't recall if this connection was ever
made, but Twain did write that pastors justified slavery in the pulpit by
pointing to Biblical passages. Likely, these would be from Paul's letters
which say much about proper behavior of both masters and slaves--not
denouncing the institution in the slightest, but rather codes of conduct on
both sides. In short, my suspicion is that Hannibal citizens heard sermons
saying slavery was morally o.k.--but to be kind and just in their treatment.