This is a very interesting question, and one more interesting still when explored in the concept of children's literature. When it comes to freedom versus agency, most would define agency as a form of freedom that is broader and more uninhibited in scope. For example, a character in a children's book may be free to make the choice of whether or not to answer an inciting call to action. However, that character may not have the agency to make that choice. To have agency, someone must not only be legally free to make a choice, but also able to make that choice without social pressure or coercion. A choice made without any other viable choices may be a "free choice" but not one that reflects agency.
For instance, take the character of Tom in Tom's Midnight Garden. His aunt and uncle have done everything they can to give him the freedom that he may desire. However, it is obvious even to Tom that he has no agency in the circumstances of his life. This is a huge contributing factor to his restlessness and misery. To give a child freedom involves letting them go into the world. To give one agency takes far more effort than that. Tom's caretakers do not remember what it is to be a child, so they have no concept of how to provide the tools to help Tom find his agency.