Since you are married the only filing status you can use is either Married Filing Joint or Married filing Separate. In both cases, you would have to have an ITIN for your spouse.
Because she has been here more that 180 days total she would be treated as resident for tax purposes.
You will need to apply for an ITIN for her, she does not need to do it herself i.e. as long as all the documents are in order and she has signed she does not need to be here for receiving the ITIN. Easiest way to do that would beto file your 2015 retrun including her as spouse, Married filing joint and along with it include the application for ITIN -- W-7. I understand this probably means in your case that you have to file an amended return but that is OK -- you probably have to go to a local IRS walk--in center with her passport and other indentification etc.
Once this is in the system , she can go back to India -- but this will allow you to get the benefits of MFJ for both 2015 and 2016.
If you need more details, please add to this thread
