I have two small children; My daughter was 5 when I came out, my son 2. They're 7 and 4 now... Something I realized fairly soon into my transition is that no one was going to have warm fuzzy feelings about be being a Transsexual parent. What's most frustrating is when being Transsexual is associated too closely with sexuality.... It's an unfortunate fact that lots of people make the assumption that we're trying to satisfy a sexual need and that we should be hidden away with the porn.
Because you're Trans, there will be frequent obstacles that you and their Mom will have to overcome. If a split is imminent, so be it, but that doesn't mean that she has the right to tell an outright lie to your daughter.... Don't let that slide! You need to have a serious discussion with your wife on how things are going to proceed with your kids ASAP. Right now, in early transition, everyone in your life thinks that you've completely lost your mind... Just accept that and concentrate on real solutions. Maybe you could start seeing a therapist as a group to work on constructive ways of dealing with everyone's issues. You might also want to start looking for a GLBT or Trans-friendly lawyer so you are at least aware of your rights.
My wife stated that she wanted a divorce in the same conversation as when I came out to her. The issues with her and how things were going to be handled with our kids took a long time and lots of hard work to resolve. It didn't look good at times.... Now, I'm over a year into living full time and worked just about everything out. I have a great relationship with my kids and spend lots of time with them. I knew things would be ok when my daughter asked out of the blue, "Jess, can I braid your hair?" I almost cried.
I know that today was a bad day and you're probably going to have lots of them before you're through this wild ride but don't get too discouraged. We Transsexual folks are some of the most resilient and courageous around! You can do this!! :-)
Jess