Yes, I believe Jack's comment is a clear indication that he is aware of his relationship to Aaron. That comment was inserted so that the viewers would understand that he knows. Now I wonder how he found out. It may be that Christian tells Claire that Jack is his son, then she tells Jack before she dies. Or due to the publicity about all of the passengers, Jack may find out after he gets back.

This knowledge that he is related to Aaron - I still do not see how that would make him initially refuse to live with Kate, or even visit the house. I think he must have gotten the message that "he should not raise Aaron" before Hurley told him. His reaction seemed to indicate that it was not the first time he had heard that.