I think... it might be best to walk away from the relationship and return to being friends. If you were more invested in this relationship my advice would be different (and I don't mean b/c it's been too short a time, but because you agreed to a casual affair), but as it is, there are two dealbreakers already : you aren't interested in women/aren't bisexual, and you want to be dating/sleeping with a man. The first isn't fair to you, and the second isn't fair to her.
There *are* people who manage to make it work despite those conditions, but it's a HUGE amount of work and compromise and suffering, and you have to be sure you're willing to commit to all of that (with someone who won't commit to you!). If you're falling in love now, it's going to hurt a lot more later on to let go of her when she transitions - which I'm assuming is what would happen only because you've said you want to "enjoy him." When "him" is gone, you'll want to move on? And how long will you actually be able to *enjoy* this when you know she's doing something that makes her unhappy, which (to your credit) you're already aware of?

In the end, though, the really important advice is to talk to her and see what she wants and expects. I mean, it sounds like she's made that clear with the "casual" thing, but you can ask whether she even wants to try maintaining a relationship once she's begun to transition and isn't willing to appear as "him" anymore. Especially because HRT can change a lot; if you're having trouble with how much she looks like a woman now, you should be prepared for the fact that HRT will most likely cause her to look *even more* feminine and less like the guy you met, until you probably won't be able to imagine that guy even when she's performing male drag for you [if she's still willing]. By about six months on HRT, my wife couldn't pass for a guy no matter how hard she tried, not even to those of us who remembered her before.
BTW, just as a small note so you don't get jumped on in the future, it's usually more polite not to say "a mtf" and "a transgender." (She's a trans woman.)