Yes it's a very good idea you never say anything negative about the org directly, but rather speak to a general call to being "well informed" or something like that. I knew somebody had to be encouraging her, people just don't decide one day that have to take the plunge!
The last thing you need is for her to think that you are an agent of satan. When somebody is in the works towards baptism they are told over and over again satan is going to use people to try an break their faith. Don't fall into the trap of fulfilling that lame, fake, and predictiable "prophecy". There are many ways around it and I'm sure you'll do well.