How about this:

1. You start your GC process.  
2. Put her name as your spouse although you two are not married yet.  
3. Continue the application process as a married couple.  
4. When the time comes for interview ( I understand this is one of the steps towards the end of the GC process), have her go to Nepal and get a new passport.  I don't think any record is kept on when one leaves the country.  So she could very well have returned to Nepal before she became out-of-status (I hate the word illegal, she did no illegal stuff so she ain't illegal).  Since now she has a new passport, there is no Nepali Immigration's re-entry stamp either.
5. Acquire a marriage certificate that is retroactively dated (as listed in your GC application).  
6. Go to the interview together as a couple.  
7. Come back to the USofA as a brand new husband and wife.

This might be a loophole that you can benefit from.  Just to be clear, I am not recommending you do anything illegal.  But if there is a way that satisfies all parties, as this might turn out to be, heck, why not.   Obviously you love her and she loves you, I presume.  And as that corny cliche goes, "Give Love all the Chance it needs."