It doesn’t sound like you were living as brother and sister the last 12 years. If that were the case, you could have confessed the marriage outside the Church and nothing would have kept you from Communion.
No, the fact that your family is Presbyterian does not make the marriage invalid. The marriage is invalid because you, as a Catholic, married outside the Church. When you are married in the Church, assuming you get the proper permissions to marry a non-Catholic, you will have a valid and Sacramental marriage. I hope that happens soon so you can end this wondering and get on with being married and being Catholic.