I seem to get very down about the fact that I see my adoptive children being raised as Jehovah's Witnesses.
A couple of things stood out in the OP. One, you say 'adoptive' children. This could mean that you and your wfe did adopt two children, in which case you would perhaps be less likely to call them adoptive and just say 'children'. I could be wrong but I suspect they're your step-children in which case you have very little rights to access (even if they were your biological children you would still have suprisingly little in the way of rights). Anything you do which may cause your wife to have doubts about your influence on them is likely to cause you an issue with access.
Secondly, you say that 'you' get very down about it. This doesn't mean that your kids are down about it. I suspect they are leading a happy life and are being well cared for. Any doubts or conflicts you raise with your children now, at a time in their life when they are totally dependent on their mother and are absolutely unable to do anything about it, is going to have a upsetting affect on them.
Perhaps keeping your feelings about the JWs in check until they are of an age when they can make their own decisions is the best thing to do for the kids.
The only caveat I would make about that is with regard to baptism, if that rears its head before they are of a sensible age I would bring it up with their mother.