This is an interesting question for a number of reasons, the first being that "freedom" is not an automatically obvious theme contained within this work that has so much to do with colonialism and moral corruption. Therefore in responding to your question I will refer to freedom in the slightly different context of self-knowledge, as becoming aware of yourself and your acts and what they have resulted in is a form of freedom - a moment of self-realisation.
It is easy therefore to discuss freedom in the context of one of the novel's major themes, which is moral corruption. Arguably, this in itself encompasses many other themes such as racism, loneliness and madness, because each of these result in the moral depravity revealed by Kurtz and his acts in the "heart of darkness." It is clear through what we are told in the novel that Kurtz has become depraved and lost all reason in his desire to gain more ivory and rule. It is clear that internally he has given himself over to evil and acts of horrendous cruelty and violence. Conrad suggests that this moral failure is both a result of the setting - the isolation and loneliness away from "civilization", but also the fact that in all of us these evil instincts are waiting for an opportunity to emerge. It is never clear, but one key moment of freedom could be when Kurtz on his death-bed is given the insight to see what he has become as he utters the famous lines "The horror! The horror!"
Self-realisation and freedom is not limited just to Kurtz, however, as Marlow has a similar moment of freedom when he realises that he is capable of descending to the same depths of Kurtz because of his own innate propensity to commit terrible acts.
Freedom, therefore, whilst not necessarily being the most obvious theme, can be fruitfully discussed through the analysis of self-revelation and moments of epiphany such as those experienced by Kurtz and Marlow.