Seems to be pretty futile to give you more feedback at this point since you haven't responded at all. But, because I hope you'll come back and continue this conversation, I'll chime in.
First of all, I'm genuinely confused. Do you suspect that she's lying to you about any part of her story? Let's be clear: if she was drugged, she was raped (from not only an ethical standpoint, but also a legal one).
I often hear this type of rape (in which the victim was drugged or incapacitated) referred to as "nonviolent rape." Although you didn't say it explicitly, it sounds to me like this is how you conceptualize it. Defenders of that term argue that it's important to differentiate "non-violent" rape from the "violent" kind, the implication being that rape doesn't really count as real rape unless the victim is severely beaten or threatened with a gun.
The problem with that term (and mindset) is that, by definition1 , all rape is violent. It's always physically and emotionally painful, terrifying, degrading, and deeply scarring to be forcibly sexually violated. You said that she's handling it well, and I don't doubt that, but you can't lose sight of the gravity of what's happened here.
1 vi·o·lence ˈvī(ə)ləns/Submit noun behavior involving physical force intended to hurt, damage, or kill someone or something.
Your retelling of these events includes a lot of information about your own behavior. It's unclear whether you've included these details out of genuine self-awareness or a complete lack thereof. Just so that we're clear:
At this point I wrote her off in my drunkenness because I was denied my midnight kiss. I yell "Fuck you!" Then go back to get my friend to confront this guy afraid of what I would do.
This is embarrassingly bad behavior on your part. It was also wrong of you to disclose the fact that she'd been raped to your friends and family (I understand that they were probably at the NYE party, but it still sounds like you weren't adequately discreet about this highly sensitive information).
I still can't figure out why you suspect her of any wrongdoing to begin with. Who cheats on their brand-new boyfriend with an unattractive dude (your words) in front of him? What reason would she possibly have for doing that? You've worked with her for a year, would you have started dating her if you'd had any indication that she might do something so irrational?