Schedule a consultation with an experienced immigration lawyer. From what you have written, it appears that she would qualify to adjust status without leaving the United States. She should not leave the United States without speaking to an immigration lawyer.
You should consult an immigration lawyer to discuss the specific charge, the date it occurred and its exact disposition. Only then would an immigration lawyer be able to advise you whether you should apply for naturalization.
In order to even being to answer your question, you would need to provide some basic information as to your status here in the U.S. What status are you here on, if any? Are any petitions pending with USCIS or the Department of State for you? Are you a Lawful Permanent Resident with a 10 year Permanent Resident Card or a Conditional Resident with a 2-year card?
So long as the marriage was bona fide, it does not appear based on the facts you have provided that citizenship will be withheld. However, I would strongly suggest that you consult and retain an immigration lawyer to assist you. Immigration law is complicated and the stakes are high. There is no reason to go it alone. Some people apply for citizenship on their own and end up in Removal proceedings.
If you appreciate the time spent preparing this answer, kindly consider marking it BEST ANSWER...
You may wish to schedule a consultation with a lawyer. Good luck!
The Murray Law Firm
50 Harrison Street, Suite 310F
Hoboken, NJ 07030-6151
Facebook: http://www.facebook.com/MurrayLawNJ (Follow by clicking the "Like" button")