On writing your mother a letter: I think that it would be a good idea to let her know very clearly in writing that you respect her and want her to be part of your children's lives, but she must reciprocate that respect. This is a civil, reasonable, and fair expectation of anyone.
Perhaps she does not have to agree with your decision to leave the JWs, but if she wants to be in your children's lives she must not "shun" you particularly in front of your own children due to her disagreement. Rather, she needs to contribute to the welfare of your children and unity of your family by respecting you as their parent and mother.
I know you aren't particularly concerned about her teaching the children JW things when they are with her, and maybe this is because you are willing to overlook more than you normally would for the sake of their relationship. But, at some point your children will be old enough to understand JW teachings such as birthdays are evil and Armageddon, etc. These teachings could affect your children. I don't know about you, but I certainly wouldn't want to impose that propaganda on anyone much less young, impressionable minds. It may be worth asking your mother to bond with your children in ways other than religious--or at least refrain from certain teachings that you believe could be damaging.
Hopefully she would read a letter if you wrote one, but I wouldnt rely on her doing so. She may read it and refuse to comply. In this case, hope for the best, but prepare for the worst. Do all in your power to surround your children with good people who share your values and respect you. In my case, I joined a local church group for a time and made a lot of friends. I don't attend the church, and most of them don't either, but at least I have a great support group! Much better than anything I had at the KH.
You and your children deserve much better than what your family has shown.
I apologize this is such a long post.
Edit: as for a biblical appeal, I would not divulge any scriptural basis on your demand for respect. First of all, no one needs a scripture to agree that shunning a parent in their children's presence is disrespectful. To ask someone to treat you humanely is not an unreasonable request and does not require scriptural backing. Secondly, JWs are conditioned to only look to the FDS for interpretation of scripture so anyone-particularly a DF'd person-who quotes the Bible will be seen as misinterpreting scripture. I could go on, but I'm stopping here.