We will never know all that happened on that overnight but in the suit the captain stated a few things that stand out. These are things he did not dispute:
She was in his hotel room.
He missed a call from crew scheduling on his cell phone (as opposed to his phone wasn’t on).
He answered a phone call from CS about their cut off time and got the time mixed up.
The fact the Copilot doesn’t work for Alaska anymore and the allegations of a second alcohol related incident certainly don’t put her in a positive light.
Still, why did they get a two calls during their rest about alcohol usage? You have to wonder who saw what for that to happen. Also the captain’s claim his cellphone was still on the wrong time zone after he missed a call is not very believable, the first thing every phone does when it reconnects is update to the local time.
As far as consent, the way the law works: if you are too drunk to positively give consent, and you end up having sex, you are getting raped, regardless of what sex you are. So, yes, if both of you are too drunk to make a decision and end up in bed together, the first person to cry wolf afterwards has a legal case.
Again, I don’t know what happened, and I am definitely not sure if he should have been fired (especially after she left under “circumstances”), but he isn’t telling the whole story either.

Feel free to correct me if I have any of the facts wrong, I don’t have a personal attachment to the case.