Sarah,
First off let me give you some hugs. *hugs* You were very brave in telling your wife. And yes, you *did* need to tell her. Keeping it a secret and creating a "secret" life are not the way to go. If you thought your wife's reaction was bad the first time, when she finds out your "secret" life, the resulting explosion will be incomparable. So, I don't recommend the "secret life" route. For marriages to survive, you need to be honest and keep the lines of communication open.
Marriages can and do survive transition.
As sneakersjay said, your wife needs more time. When a person realizes they are transsexual, it's like having a bomb dropped on the spouse sometimes. Gather up some information and ask your therapist for some advice on broaching the subject with your wife again. I don't know if this will help, but one of the things Dani did for me was open up a "listening line". Where she just listened to what I wanted to talk about regarding transition. The important thing is that there were no arguments or blame or anything; she just listened.
As an SO, I can totally understand your wife's reaction. It's fairly normal. In no way should you treat it as a "reason" to go back into the closet. When our spouses tell us they they want to change their genders, it creates a whole lot of strong, conflicting feelings, which take a while to sort out. Anger is there, grief is there, sadness, confusion, pain...SO's have to do a lot of thinking in the initial stages. Your wife's probably thinking about how people will perceive her and how family will react. She'll be thinking how to tell your son, and what about work and school? She may think of it as a threat to her "womanhood", that you'll somehow be "better". She may also have phobias about lesbians, due to high amounts of misinformation put out by a host of religious institutions. She may also think that you want to change overnight (and even if you do, I suggest keeping to a pace your wife is comfortable with.) Or she may be thinking stuff I can't even guess at. This is where that listening line and having information ready can help...so you can learn what your wife is thinking and have info handy to help calm her fears.
You may want to suggest therapy for your wife as well, so she has a safe place to talk about things. I also *highly* recommend couple's sessions. As Dani (my spouse) said, this ultimately is about *us*.
Let us know how it goes, OK? I hope I was able to give you a bit of insight as to what your wife may be feeling. Don't give up!
WR