Hi there !! My dad said some thing to me that really stuck, the church is a perfect place full of inperfect people. And it is so true!!! Far too many people loose faith because of what he said or what she did.
I'd have a talk to your boyfriend discuss with him what missionairies should and shouldn't be doing. Don't make the decisions for him but just inform him, it sounds as though he doesn't know any better.
As for the stake president well, some times I hear people say things that strike me but arn't really intednded to be about me. I'd say do not dwell on the mistakes your stake president has made but look for good qualities in him and you might be suprised.
Well done for coming back, I also came back to church and life is so much better for it !!!