There are several problems with this. Leaving the wife without agreement is abandonment and any decisions reached by the courts would look more favorable on the wife.
Taking the children without an agreement would be considered kidnaping and jail time would be very possible for the party that takes the kids.
Your response if ask should be to discuss it with the wife. If it results in divorce, the court will resolve the issue of the kids and money. There is a possibility the the wife will chose to remain married with your friend allowed to transition when force to make a decision.
In any case, the first thing your friend should do is see a divorce lawyer. The advice will prevent many problems latter on if things get hostile.
I agree they shouldn't live in the closet but they should come out legally or they may end up in jail without the ability to transition. Unfortunately there aren't always happy endings but playing by the rules prevent them from becoming disasters.