Hey Greywolf,
Almost everyone feels some sort of discomfort and reservations when they first get into BDSM, because it is so taboo and so many vanilla people think that it's "wrong". But the fact is that you are who you are and you have to accept yourself, you have to learn to be comfortable with yourself, because you are stuck living with yourself 24/7 no matter what kind of life you choose (advice from my good ol' mom). I also was raised in a Christian house, but it was a liberal Christian house with the attitude of God made you who you are and he's not ashamed of you, so you shouldn't be. It takes time for a person to get used to any new idea, so don't worry about it, take it slow, and it's wonderful that you have a partner who is able and willing to go through your self-discovery with you! And yes, so long as you work towards it you will become more comfortable with yourself, just as would happen with any other change in life.