Well, speaking as a mom of three, with JW parents (my never-JW in-laws passed away a long time ago) I can empathize with your situation. My husband and I were still JWs when our children came along, so we didn't face the dilemma that you have now, before you even have children.
However, when we decided to stop attending meetings, the atmosphere with my parents cooled down a lot. Especially after an episode where my dad took it upon himself to discipline my just turned 6 year old daughter very harshly in front of a dozen onlookers. We did not speak for almost 2 years, because I had the audacity to stand up to him on behalf of my children and not allow him to humiliate my daughter the way he did.
I think the best way to deal with the situation is to say, right from the outset, that you have no intention of bringing the children up as JWs, and that you expect them to respect your decision. If they want contact with their grandchildren - which you will supervise - they will have to abide by that. They have shunned you anyway, and basically they will either respect your parental decision, or they will go back to their shunning behaviour. Do you really want that kind of conditional love from your parents toward your children??
My own children don't have the kind of relationship that other kids have with their grandparents. They get no gifts from them. Ever. They've never had a story read to them by their grandma or grandpa. To my kids, grandma and grandpa are nowhere near the top of their list of favorite people, and it's obvious (to me at least) that my kids are nowhere near the top of grandma & grandpa's list of favorite people. My parents would rather get together with their JW friends whom they see at least 3 times a week, than spend quality time with their grandchildren. It was that way even when we were still JWs. So I don't feel any guilt about limiting the time my children spend with them, because they don't seem to want to spend time with them anyway.
Remember, once you've had children, they need you to advocate for them - and if you don't want JW interference in their lives, put your foot down from the start. If they disrespect your wishes, do the same thing to them as they have done to you - shun them.
Love, Scully