Why doesn't she qualify for naturalization (married to a u.s. citizen?)
Specifically, there's a minimum residency period before you can apply - usually 5 years, 3 if you're married. The conditional greencard is the first 18(? 24?) months, before you get the 10yr card - so if they're still conditional, there's no way they meet any minimums.
The path from marriage to citizenship is not automatic (nor inalienable).