Certainly. When approaching this assignment, it will be best to first look at the circumstances surrounding the concept of "freedom" in each of the works by exploring the similarities and differences in the lives of the primary characters.
First, in the case of The Sorcerer's Stone, you will be exploring a story that is considered to be "high" or "hard" fantasy. This means that the world of the narrative is entirely fantastical. Because of this, the protagonists will face physical struggles completely alien to you or me, but these struggles will reflect real emotional and mental ones that we experience every day. In the case of Harry Potter, his lack of freedom stems from a stifling of his real identity. His past has been kept a secret from him by his abusive aunt and uncle, and only through escaping into the world in which he truly belongs can he experience true freedom.
Secondly, you mentioned Tom's Midnight Garden, which is a work of "low" or "soft" fantasy. This means that while the story contains some supernatural or fantastical elements, the narrative is overwhelmingly rooted in reality. Similar to Harry, Tom finds himself in an uncomfortable position in a house with less-than-desirable relatives. Tom, however, suffers none of the abuse or neglect that Harry does, and does not have a grand destiny. Tom's struggle with freedom is entirely personal, and deals with his relatives' incapability rather than unwillingness to understand. He is isolated, but the solution is less readily obvious.
In the case of Roll of Thunder, Hear My Cry, we are dealing with a work that is entirely rooted in realism. Cassie's struggle with freedom is the struggle with the Jim Crow-era South. Her struggles are not mysterious or personal, but very plainly present and threatening in her day to day life. Cassie cannot afford to be complacent or shy, she will only attain her freedom through acts of repeated defiance. Her struggle is a collective one with the entirety of the black population of the South.
All of these characters are quite different from one another, but they do have some things in common, all of their experiences reflect a coming of age, and only by growing up and abandoning illusions present from childhood can they reach a legitimate chance at true freedom. A thesis might look something like this:
Though their struggles revolve around vastly different circumstances and even worlds, Harry Potter, Tom Long, and Cassie Logan all must abandon the preconceived notions of their predecessors and come of age on their own terms in order to understand the true notion of freedom.