Well, you are in an unfortunate situation. I’m not going to rake you over the coals, here, but you should understand how your obligations break down, etiquette-wise:
1) You are completely correct that an STD is an obligation. So once you sent her an STD, you were absolutely obligated to invite her, there is no question there. If you had cut her from the list *after* sending her the STD, that would have been terrifically rude (and I’m sure more hurtful than the current situation).
2) However, just because the STD is sent when she is single does not mean that you’re allowed to invite her ‘singly’ if she is in an established social unit recognized by etiquette at the time the actual invitations get sent out. (Try to imagine if she had actually eloped – not inviting a spouse? Hard to justify!)
These are two principle of standard etiquette – I realize they, combined, are somewhat burdensome for hosts, but frankly etiquette often is. If it were all easy as pie, then there wouldn’t have to be etiquette rules reminding us of our obligations. 🙂
Ideally, a host would select a venue that had enough ‘wiggle room’ in capacity above their theoretical max guest list that something like a friend’s new social unit partner would not break fire codes. But, what’s done is done – either you chose a venue a little unrealistically with too tight a cap, or (what it sounds more like) all of your wiggle room got eaten up by other issues. If the latter, nothing to be done about that now.
Now, I will say that if those ‘things that ate up the wiggle room’ occurred *AFTER* this couple moved in together, then you’re on shakier ground in terms of what you should have done – simply because the instant *you were aware* that they moved in, he should have been added to the list if it were physically allowable in the venue at that moment. (And no, you don’t have to be a mindreader – if she didn’t tell you for a month, then your obligation began the moment she *told* you).
But, assuming that the moment you found out about the cohabitation you were already literally *at capacity* on who you were obligated to invite, the best thing to have done before sending the invitations out would have been to let your friend know. Since technically you were going to be violating a rule of etiquette, but there was simply no way you could avoid it, letting her know with a direct phone call and a quick apology could have seriously softened the blow. Etiquette rules get broken sometimes. We should strive to avoid it, and we should not just throw them out the window at our own earliest convenience, but sometimes we find ourselves in an unfortunate situation (sometimes of our own making) where we simply no longer have a choice. “Friend, I am terribly sorry about this, but turns out that we managed to overbook the venue, and that was before The Dude appeared on the scene – I’m trying my *best* to fit him in, but at this moment, I’m afraid I have to send your invitation to you alone. But I promise, if I can invite him without violating fire codes, I will let you know *immediately*!”
Saying that *before* the invitations go out is more respectful of your friend: it acknowledges her relationship and your obligation, and would avoided the awkwardness of her having to seek you out to see if you made a mistake in the addressing. And I would hold to what is said there – you *do* have an obligation to try your best to include him. The first spot open should go to him, unless you actually have more people you are *required* by etiquette to invite and haven’t: he is not just in a ‘we’ll try to accommodate them’ category of people you’d like to include if you can.
So, there may have been some poor planning on your part (in terms of venue and capacity), but we all make mistakes, weddings are hard to plan, and hindsight is 20/20. I think your primary mistake here was not being proactive in letting your friend know the situation before the invitations went out, and taking the lead with an apology for the situation. That alone could have saved you a lot of hurt feeling and awkwardness between you and your friend. Your obligation going forward is to give him the first spot that is available, regardless of the other people you’d prefer to include that aren’t on the list yet.