Will my wife have to leave the US since her passport expired?

As long as you married within 90 days, you are still eligible to process her adjustment of status through the K-1 petition. You may want to speak to an experienced immigration attorney who can assist you with the process.

You can still file in the US without getting a new passport. If done right, the entire process should only take about 3 months. And your wife does not have to leave the US.

It is not too late to file her adjustment. It is usually a very simple process. She can only adjust though you. It does't matter that her passport is now expired. What matter was that, at the time she arrived in the US, the passport was valid, her visa was valid, and she received her I-94. Please do not send her back to her country...there is a law indicating she would be banned for 10 years because she overstayed for more than one year. (She started cumulating unlawful presence after her 90-day permission expired.) I hope this helped.

I would suggest that you hire me to get your wife her green card, asap. I rarely would suggest that anyone leave the country because of the severe penalties for those who leave, but there are always exceptions depending on particular facts of the case.