I agree that this is something the church should think about. In an ideal world, a person wouldn't go through transition only to change their mind later, just as in an ideal world there wouldn't be divorce. But human beings are imperfect and make mistakes, and the church needs to think about how to deal with messy situations.
On reflection, I don't think our church has a ceremonial rite for divorce, either, even though we have many divorced church members. There's still a lot to figure out.
The Anglican tradition, like yours, sees baptism as occurring only once. So whatever rite the Church of England constructs, it won't be a re-baptism, or any kind of repudiation of one's earlier baptism. It might involve a reaffirmation of one's baptismal vows, but that's a different matter. Our tradition has a number of occasions (such as confirmation or returning to the church after a time of unbelief) on which one says, effectively, "Now that I've gone through this change in my life, I want to affirm that I'm still a Christian and recommit myself to Jesus." Such a reaffirmation isn't seen as any kind of rebaptism.
So, the original baptism would still be seen as the one and only baptism in the person's life.
I haven't yet seen any draft liturgies for gender transition. It'll be interesting to see what they come up with.
