My mom was baptized when I was two and my dad is not a witness. I am out but I have a younger brother and sister (now in their 20's) who are still in. When we were very young, my dad did make a stand about us not being allowed to go out in service and not being allowed to go to evening meetings. I do remember, especially in the earlier years, that my mom and dad would argue a lot about doctrinal stuff and I'd usually think that my dad made the most sense (of course, I could never tell my mom that). But by the time I was in mid-elementary school my mom had wore him down and we were completely consumed by witness activities. My dad more or less wimped out. The only time he put up a fuss was when I got baptized when I was 16. By the time my brother got baptized when he was 12, my dad didn't say much of anything.
When I was having the most doubts (age 12-15, I would say), I remember wishing that my dad would step in and exercise a little bit of authority. I hated going out in service and to the meetings, but I was afraid to stand up to my mom. I remember in junior high, in particular, I felt like I had nothing in common with the witness kids my age and I had a very good friend at school who my mom wouldn't let me hang out with. I remember wanting to do after school activities and go to dances and my mom said no. If only my dad had stood up to my mom, I think my life would have turned out very differently. My dad never did anything and I eventually ended up just getting sucked in (I just sort of bottled up all the doubts).
I remember that there was an elder in our congregation who had a good job who had been raised as a witness in a divided household. His dad made him go to college. Even in high school, after I had gotten baptized, I remember always hoping that my dad would actually put his foot down and MAKE me go to college, but he never did. Of course, being the good witness girl, I worked part time for minimum wage and pioneered after high school. Because my dad had become so "hands-off" about it all (and his arguing with my mom about doctrinal issues in earlier years had turned him into an "opposer") it somehow turned the whole household dynamic into an "us" (mom and the kids) vs. "him" situation, even though I had SO many doubts about witness stuff.
I guess my advice, based on my experience, is that although you don't want to be an "opposing" mate (and I agree, this is especially important initially), you definitely need to provide options for your kids. If you feel that you can, present an alternate view on doctrinal issues to them privately (don't turn it into an argument with your wife). You'd be surprised at how many doctrinal issues don't make sense to kids at even a very early age (at least, they didn't to me). Make a point to let them do things with non-witness friends. Celebrate the holidays. Encourage non-witness after school activities. Let them play sports. Take them to another church with a good pastor once in a while. Do anything you can do to broaden their horizons. I can tell you from experience that when you've been raised as a witness with no options it is VERY hard to get out (it took me 8 years after I was baptized), even if doubts were present from a young age.
You sound like a caring, concerned dad. Hang in there and good luck!