The expired I-94 is ALL RIGHT for purposes of applying for her permanent residence on the basis of marriage to a US citizen. You cannot get a new I-94 because of the overstay but even if you could, it is not necessary. However, it is absolutely NOT all right for her to travel internationally until after her permanent residence status is approved. Do not even apply for the advance parole travel document because she will be issued the document if you apply for one but she will be BARRED from the US for a period of 3 or 10 years because of the overstay. If you are paying a lawyer to do this for you, I think you have either selected a very poor choice for a legal representative or you are not posting all that your attorney advised here. ANYONE with any kind of experience in immigration law would be able to tell you that your wife SHOULD NOT use an advance parole if she has been unlawfully present in the US for more than 180 days prior to the filing of the adjustment of status. You'll either go to the wedding in Canada on your own or you won't go. If you go to your wife, she will be in Canada for a lot longer than both of you may anticipate.
Don't go on with your arguments about legality v. reality. They are really silly and irrelevant. The reality you are talking about may be YOUR reality, but the legality is THE reality that your wife will be facing if she goes abroad before her permanent residence status is approved. I think that if you have not been so advised by your attorney, this is really bordering on malpractice, but then again, if you are only using a paralegal service and not an attorney who is duly licensed, then you are doing yourself a great disservice.
Please let me know if you have any additional questions or how I can be of further assistance to you in this matter.
Admitted to practice in CA, AZ, IN and OH