Daniel
It is good that you told about your feelings. I can understand your feelings more than you might think.
My marriage broke because of a similar situation. My wife left, because she couldn't accept, that I got different feelings about JW teachings like blood, shunning, inspiration of bible etc. She said if I don't accept it as the gb is teaching, she can't live with me any longer. Now we are divorced, she tried everything in her power to limit my time with our wonderful little son and she is indoctrinating him strongly. But my son and I have a strong bond of love, which cannot be torn apart.
When I read your experience, it seems to me that despite all problems, you and your wife love each other. That is the best basis for your marriage. You said your wife isn't that active with jw things. So there might be a chance that her feelings might change about this religion.
I would suggest not to overwhelm her with anti JW reasoning. But slowly you can sow seeds of doubt. For example birthdays.
Make it known to her, that the birthday of your children are days worth celebrating, because as parents it was the most important day of your lives when your children were born.
Maybe ask her how she feels about the day when they were born. Make it known to her that she is a good mother and that you are thankful for everything she endured on the day your kids were born and that it is a day worth remembering even celebrating.
By the way the bible doesn't say anything against it. On the contrary. Romans 14:1-5 says that it is a conscience matter which days to remember. Even Jobs children celebrated birthdays according to Job 1:4. That the day of birth was meant is confirmed in Job 3:1.
If the tension in your marriage persists, marriage counselling would be a good idea.
Anyway I think of you and I hope that you find solutions that work for you and your family. But don't rush. Be patient.
I wish you all the best.