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I think that Pip's reasons for acting in this way can be summed up by the following sentence from the start of Chapter 47. Here, Pip says that
I had quite determined that it would be a heartless fraud to take more money from my patron in the existing state of my uncertain thoughts and plans.
Pip is giving the money back because he does not want to be hypocritical. He does not want to take money from someone that he looks down on. Now that he knows the money comes from a criminal, he does not want it because he is too good for that (this is like how he does not want to acknowledge Joe -- he thinks he is above his former status).