Hi Rebecca
There are enlightened, accepting churches out there. I attend a MCC/UCC affiliated church and my girlfriend who is a transgender woman attends an Episcopal church in her community and both are welcoming to gender variant people. I would suggest that you make some calls and find out what churches in your area are accepting. It surprises a lot of people but being transgender and being a Christian are not mutually exclusive.
Sadly, there are a LOT of issues that keep churches from accepting us, such as ignorance, politics, tradition, defense of long established church dogma, and so on - some churches seem to be far more interested in keeping and defending the status quo instead of seeking out a deeper understanding of what their faith is about and ministering to all people.
We suffer from a medical condition that was present when we were born - none of us chose this. We are simply trying to live as best we can with what we were given.
Your partner is embarking on a journey to authenticity. She will be a far better person once she's out from under the crippling effects of gender dysphoria. She will have lots of ups and downs and stumbles on this journey and she'll need you to be there for her.
Please ask as many questions here as you would like - this is a safe place and you are among friends