Immediate relatives (notably including spouses) of U.S. citizens may apply for adjustment of status despite a period of overstaying a visa.
It may well be that her best option (if she has not yet overstayed by 180 days) is to leave before she triggers the three year period of ineligibility (after one year of overstay that becomes a ten year bar). Even if her overstay is greater than 180 days, it may turn out to be her best option; consider consulting an immigration lawyer with the details.
Otherwise, petitioning for her after naturalizing may be the best option.

