There was the option of Alyssa not transitioning. And, to me, that was the worst of the options. For her to come out of the metaphorical closet and then be shoved back in saying "and stay there!" Would not bode well. She would most likely become very depressed, angry, bitter. Her ability to be a good father would most likely suffer and she may do damaging things to herself, like drinking, to cope. I imagine we would end up divorcing from this and the children wouldn't have fond memories of a father.
Then there's the scenario of her transitioning but me leaving her, still being a friend to her. That possibility accomplishes nothing for the children. In fact, may be the worst option. I would never keep the children from Alyssa so this wouldn't "save them" from having a transgender parent. On top of that they would see both of us only part time and instead of having me stay at home they would see me only at night and every other weekend. They would essentially lose both of us and still deal with the reprocussions from this. It's simply not an option unless I truly cannot handle this transition and it becomes unhealthy for the family.
So, that leaves me with staying. Staying allows me to still be a wife and stay at home mother. If we continue to grow and be a healthy marriage it will show the kids a relationship and marriage that runs very deep and withstands almost everything. They will have both of us to love and support them.
And if our marriage doesn't make it, at the very least I can say I tried.