Your kids may resist liking your wife, even just a little, because that feels disloyal. The same sense of loyalty may exist if you divorced. To your kids, Mom wasn't all that bad. And your wife may seem like the culprit who took Mom away. Your wife is probably dealing with some shock of her own.
Most parents get to grow into the parenting role.
It's tough for a woman who never had kids suddenly to have nearly grown ones. When it comes to parental discipline, it's possible that because you can see both sides, you've failed to back up your wife's authority. It's time to upset this uneasy truce and confront the problems. Tell your wife and your sons how much you love them and for that reason things can't go on as they have. A counselor can moderate the more volatile topics of discussion.