'Uncle Tom' is a derogatory name for a black person perceived by others to be behaving in a subservient way to white authority figures (and more recently anyone collaborating with their oppressors). The term comes from the title character of Harriet Beecher Stowe's novel Uncle Tom's Cabin which was first published in 1852.
After her rape Mary Agnes admonishes Harpo for calling her by her nickname, 'Squeak'. She realises the power of names and thus reclaims her own. When Celie calls Mr._ by his actual name (Albert) at the end of the novel, she is using the same power.
Miss Millie's inability to call Sophia a "person" reflects the dehumanizing effect of racism.