If you have already started the application process then you don't need to worry so much.
Send a copy of your fee receipt, send a copy of a sponsor approval or something showing that your intention is to sponsor her permanent residency application.
She should be honest, tell the border officer that it is her intention to "visit" while you wait for her permanent residency application to be processed. It is called dual-intent.
My husband quit his job, put his belongings in storage and drove to Canada with a copy of our fee receipt and a copy of my sponsorship approval. He did not have any problems. he was given a Visit Visa record, stapled into his passport (states he cannot work or go to school and that it expires after six months).
She's coming from the states, and they are visa exempt... she is allowed to visit with the intent of living here once her permanent residency is approved.
Besides, who would pay $1040 and NOT go through with a proper application? As long as she is honest, answers their questions honestly, then she shouldn't have an issue unless the border officer is being a jerk.
Also, some people recommend that you cross the border with her, but in our case it wasn't possible. I had my cell phone on in case they wanted to phone and verify the info, but they never did. They were actually very helpful and informative.
Good luck
