I'll be really honest. I probably would have done the same thing...and have done the same thing.
When it comes to political correctness and choosing the right word or label, everyone will miss the mark. Heck, I even said "He" sometimes when it comes to God.
I believe when the Pastor said this boy will become a great man someday, she was being very uplifting to the child and to the family. It wasn't a underhanded comment of saying "I hope your boy will be a man because I hope he wont be a girl!" it had more to do with the child's character and integrity when he gets older.
And let's be honest....the odds of this child growing up to become a great woman isn't that high. I haven't seen many transgender (MtF, FtM) people out and about. I've seen many...but in ratio to the rest of the general public we are a pretty small minority of people so I don't think it was too far out there or unthoughtful with how the Pastor handled it. It was words of comfort directed towards the Parents of the newborn.
I am sure, if the time were to come where the child was struggling with their gender the Pastor will be there for the child.