First, if your wife was a JW she knows all about their ways, which IMHO are a very tight nit group, that do not mingle with outsiders. They have very odd rules to me, which I have no respect for, as they allienate their children from other kids, school activity, and just growing up normally. I am all for freedom of Religion, but this one I have no use for whatsoever, or their customs and rules. YOur wife should probably know more than anyone, what the results will be to stray from the flock, and how she will be treated. Many other cult religions do the same thing, no matter if you are flesh and blood or not. That to me separates a true religion from some controlled cult.
All that said, you failed to say one thing about what any of this, or the JW's have to do with your belief God does not exist? Maybe your wife was left with a bad taste over the customs of JW's, which is no way to judge or decide another religion or if God exists.
The sad truth is that your wife and her siblings probably will be shunned away, ostrasized, by those who rule the roost in that congregation, and to me its a sad pathetic thing when you would allow your religion to tell you to abandon your children. Again, what does that have to do with your reason for being an Atheist? Pretty obvious that your wife and her brothers, regardless of a religion that is quirky, still had a stong belief in God, so what does celebrating a birthday, or engaging in talks, have to do with changing those beliefs?
You also never said what your unbringing was, if you had some kind of religious background, or what led you to your beliefs?
One thing I know for sure, JW's live a sheltered existance, limiting exposure to any other religions to the extreme IMHO, so you as an Atheist, must really be on their least favorite list of people. You certainly picked about the most opposite of positions to be in, and imagine how your wife must be feeling? She must be living racked with guilt both from her parents shunning her, but also jumping from some life of Faith to a life of denying God. ( just read your input again, did the Mother also branch away from the JW's? Sounds like she may have from your explaination, or has she remained and shunning off the kids who strayed?)
Big question is, do you believe your ways becasue the JW's are so radical and strict in their views, or some other unrelated questions as to the existance of God? And does you wife also have that same belief, or just abandoning her JW's ties for your Atheism?