The short answer is, yes. You can pull him from RE and enroll him again when it's time for Confirmation. Most likely the priest or DRE will talk to you about what needs to happen in order to get him caught up. I think it would be very irresponsible of you to do that. There is so much he can learn about Catholicism and about his faith in those years, but that's up to you and your husband. The priest might not even ask you about the Sacrament of Reconciliation. It's not a sacrament that usually goes in the record book.
But ...
According to Church Law, he was supposed to receive the Sacrament or Reconciliation before going to communion for the first time. I realize some priests don't do that, though they usually do a "simple" reconciliation just so they can say they did, and then explain the sacrament in more detail when the kids are a little older. Maybe that's what your church does.
Have you ever considered going to RCIA? While the RCIA is the program/process for adults to become Catholic, it is more accurately a process for adults to decide whether or not they want to become Catholic. There is no commitment. It is simply a way for you to learn more about Catholicism.
The Sacrament or Reconciliation is a sacrament of HEALING. It is about turning to God during those times in our lives when we've really screwed up and need some help getting things back on track. It is a time to stop and think about our relationships and how we can heal them. It is a time to look out our behaviors and habits and think about patterns and little changes we can make in our lives to make our relationships better. It is a time to reconcile with God and with the people in our lives.
Love the way Sarah and Robert E explained it. Fabulous!!!
It makes me so sad to hear you say, "I think the whole idea is actually destructive and is the basis for the stereotypical "Catholic guilt/shame"." Your comment is based on ignorance. You say, "I don't want to debate my viewpoint on this forum. (I can do that at home with my husband!)," but that's not really fair to your husband. It sounds like you're not interested is asking him questions about Catholicism in the hopes of understanding it better, whether you agree or not. It sounds like you just want to prove to him that his religion is wrong.
If you truly support your husband's choice to be Catholic and truly want to raise your son Catholic, then learn more about Catholicism.