Sorry to hear this, oldflame. It has been said here on JWN that baptism is the first step out of the Borg. I sure hope this is true for your son and that he isn't too scarred from his experience.
Try to remain supportive of him. Even though my parents got baptised, I made the effort to keep the relationship going even though they tried to shut it down plenty of times. It has not been easy.
Today, my Father says that he wants me to help him during his declining years and not his JW 'friends'. I actually asked him who he wanted helping him. I gave him the opportunity to choose. He chose me. He says I am supportive. I try to show unconditional love. This is difficult coming from an upbringing that taught the opposite. But I saw how it didn't work in life and have chosen to be different than what the Borg tries to force people to be.
I hope you can maintain some kind of relationship with him if possible, as long as it isn't too damaging for you.