ummmm... I understand all sides but my humble opinion, since you asked. :-)
If it were a man in MOST cases it would be Dr and Mrs as with ministers Rev and Mrs.
So I would start with your FI. How does he feel what does he recommend? For me that would be the only opinion that would really matter to me.
Now, I would say on all the favors, programs and etc it should simply be YOUR NAME and HIS NAME.
But if you want to be introduced as Mr and Dr....it's your wedding do what you want!