Make your daughter independent of the Witnesses: encourage her to go to college or university, to train for a career, to make life choices for herself that do not involve WT. I realize this may be difficult now that she has decided to join the organization, but she's young, and being part of a "divided" family may be a saving grace, she can "blame" you if any JW objects! :)
Desensitize: find ways to speak about disfellowshipping as though it were a "normal" part of living, teach her that at some point individuals will clash, and the result may be that those with power (not authority!) try to cause unbearable shame in efforts to control the life of another. Remind her that no human is her judge, that when (not if, but when) it happens to her, that she should stand firm (a WT expression), never relinquish control of her life to another human, and that you will support her no matter what anyone thinks, says, or does to mar her reputation. If you start now, while she is only 16, your daughter may not feel as alone as Elders will want her to feel if she should happen to be scrutinized in the future.
Additionally, if you have the wherewithal, make it clear to her and to any others that under no circumstances will you allow your daughter to be "counseled" without you being present, and that includes judicial matters. This is your legal right since she is not of age to be considered a legal adult. If you've been reading this board for any length of time you may already know of the horror stories, the intimidation, the extremely intimate and personal questions that are often and inappropriately asked during these sessions. Make no mistake; there is no such thing as an unintentional session; if a JW gets called in to talk with the brothers there will be intimidation and manipulation, no matter what the issue or how removed from it she may be. Train your daughter to say that she must get permission from her father before she is allowed to meet in closed session. (That one makes sense in a non-JW situation as well.)
If possible, slowly build the notion that being involved with JW's is an open-exit choice, that just as she made the choice to join, she can make the choice to leave whenever she finds that her views and theirs are no longer compatible. Don't let WT be the only one "indoctrinating" her on that point! The main message here is that she directs her life, that you are there to assist her until she reaches full maturity, and that there is no shame in trying out various options then letting them go when she finds they no longer fit.
The best hope you have is that she is still young and has lots of changes left to go through. The goal here is to let her know, in advance, that you are there to love and support her as she learns to stand on her own two feet. If she has that fixed in the back of her mind I doubt that she will put up with WT for the long haul.
Best wishes,
AnneB