This is a problem. Most who come into the U.S. without a visa must return to a U.S. Embassy or consulate to process their immigrant visas. However, if she leaves the U.S., then she can be banned from coming back to the U.S. for ten years. It does not necessarily matter that she is married to a U.S. Citizen.
You must prove, to the satisfaction of the a consular official (among others), that you will suffer extreme hardship as a matter of both discretion and law. Otherwise, she cannot legally return. If she unlawfully returns after a denial, then this can mess up matters even more.
In order to get the legal advice that you need, you should schedule an appointment with a very experienced and ethical immigration attorney. You should be prepared to live in Mexico for the next ten years where she decides to leave the U.S. Not everyone has proven that their U.S. Citizen spouse will actually suffer extreme hardship as a matter of discretion.
The above is general information and does not create an attorney client relationship.
I will concur with the previous lawyer's response. You should coordinate a consultation with an immigration lawyer to discuss the probability of success for your wife's waiver. In the alternative, you may consider simply filing the petition and waiting for a some change in the law.
Best of luck.