Is there any reason why your wife can't enter into Canada? You're able to enter and leave with an Outland application under normal circumstances. The reality is that her passport isn't associated yet with the PR since your application hasn't begun processing. So, even if you had a fear they wouldn't let her in, there's still time before they do enter that into their systems.
I've also heard some people in the past have a similar situation to yours, and their app was placed back in the queue. I'm not sure if that's the case always, but I know it's possible. (Perhaps you can indicate that somewhere on the box/package that it's resubmitted application for "missing" documents.)
Definitely include a cover letter stating what happened. I know I'd have a hard time remaining diplomatic in a letter like that, but hopefully someone will see it and feel that they need to expedite your application for their mistake. If you're inclined, there's a place to leave feedback for the CIC on their site. Definitely let them know this was their error/incompetence.
Chin up!
