Well, you were in an awkward situation because you did legit have to use her legal name in some contexts, which is not your fault. And at that point, the rest is awkward no matter *what* you do. So this part of my comment is just validation that you did the best you could with a bad hand you'd been dealt.

You are now more or less in the position I was, despite your good intentions - you were unable to start with the default assumption that she was a woman, and you're going to have to "come out" about her transition somehow. At work I honestly just switched to new name and pronouns with people I didn't know, and I hear some got the explanation through the gossip grapevine and some assumed I'd gotten divorced and remarried (and some, I imagine, didn't care enough to think about it). With the people I did know a little better, I basically said outright "Look, this is awkward, and I'm in this position where I have to either give you TMI relative to our relationship [since we don't know each other that well] or have you assume I've lost my mind by dreaming up a new spouse, so... just so you know, my spouse is the same person, but she's not identifying as male anymore, and when you hear me talk about X, that's her now." Everyone was fine with it, and I found that addressing the whole TMI/why are you telling me this aspect up front helped somewhat. In a manager's yearly review I also did say "and you might've noticed I'm talking about my wife now, which is because of blah blah insert previous canned spiel..." and we moved on from there.
As for the outing her aspect, you can talk to her about it, but the problem is that you don't have a *good* option here : you out her, or you continue to call her male forever. Tell her that either she finds a better middle ground (and who knows, she might be smarter than I am and she can!), or she gets to pick off that list, but you're not doing this maliciously and you can't figure out a better way to handle the way this impacts YOUR life.