They will let you still file married filing jointly. Unfortunately, you need to wait until the original return is processed before you amend the return. However, you will need to notify the IRS that your wife received a SSN. I asked a colleague who worked for the IRS for many years and this is his comment:
I've always thought it was just a bad idea to send in an amended return while first one hasn't finished processing; I worked in submission processing for many years and amended returns would come in -- multiple sometimes, for the same tax year -- and it would take forever for the TP to get everything sorted out correctly. Even if a detailed letter was attached to the amended, might not be seen, or detached in the mail room, things can just go wrong....
What do I do when I am assigned a social security number (SSN)?
Once you receive a SSN, you must use that number for tax purposes and discontinue using your ITIN. It is improper to use both the ITIN and the SSN assigned to the same person to file tax returns. It is your responsibility to notify the IRS so we can combine all of your tax records under one identification number. If you do not notify the IRS when you are assigned a SSN, you may not receive credit for all wages paid and taxes withheld which could reduce the amount of any refund due. You can visit a local IRS office or write a letter explaining that you have now been assigned a SSN and want your tax records combined. Include your complete name, mailing address, and ITIN along with a copy of your social security card and a copy of the CP 565, Notice of ITIN Assignment, if available. The IRS will void the ITIN and associate all prior tax information filed under the ITIN with the SSN. Send your letter to:
Internal Revenue Service
Austin, TX 73301-0057
IRS Additional ITIN Information
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