I'm in a similar but different situation.
Pardon me while I ramble, I'm a little farther along in this than you, but it's something that's still going on.
I met my partner online also, possibly around 7 or so years ago, and we've been living together for 3. So I know how you can fall in love with someone over the internets.

I'm female, and so is my partner. I was a situational lesbian for 'her', because honestly I don't like girls, and not really most guys either. My partner is my best friend, someone I can relate to, and someone I can trust. This transcends body gender.
Within in last few months my partner has realized that 'she' is alot more comfortable as a male.
It was a bit startling at the time it came out.
It DOES change things when you find something lifestyle altering about someone.
The important part is getting through the changes.
We're not there yet, but I know it's worth it.

You are already ahead of most people, you're aware that you love him for who he is. Try and keep in mind that he loves and trusts you too, after all he did tell you before his friends and his parents. Possibly when he realized how much you mean to him.
As for the physical attraction. I second Dryad. See him in person. I don't know how young you are, and if you're in a position to go visiting any time soon, but I highly recommend it, who may find him a lot more like a guy than you realize. And there's more to attraction than the physical, there really is. Seeing him face to face is the only sure way to do that.
There's no real way to tell what his family and friends will do. There are stories on both ends of the scale, just be there to support him as best you can. It'll mean the world to him.