Like everyone else has said, give it time. My gut reaction is that her saying that she is going to move away and take your child with her is borne out of the fear of the unknown. It's wonderful that you have been honest with her. The 2 of you are doing all the right things by being honest and seeing someone who can help ask the questions for you to be able to move forward.
There is always the chance that non-monogamy will always be a deal breaker for your wife. In that case the focus will have to be on your son and how to best co-parent without being married anymore. It's way too early to say if that's the way it's going to go yet.
Is there a local poly group where your wife can meet some people who are poly and who's lives are going well? Maybe even meet the mono wife of a poly man? Sometimes seeing that it can be done and it can work for everyone involved can help. (It might be too soon for such a move though...although doing the research now for when she is ready might be a good idea).
Court your wife again. Take her out places that she likes to go and do things that the 2 of you haven't done together for years. Chances are she's feeling like you want to replace her for someone younger/hotter. She needs to feel that you cherish her. For a while that might really mean going above and beyond with the romance and dating.
Hope that helps a bit.
Everything will be ok in the end. If it's not ok it's not the end.