Not sure how you could stop the ITIN process but I would not file another return until you can stop the ITIN application.   An ITIN may not be issued because a SS# has recently been issued.  

Telephone help.

If, after reading these instructions and our free publications, you’re not sure how to complete your application or have additional questions, call 800-829-1040 if you’re in the United States. If you’re outside of the United States, call 267-941-1000 (not a toll-free number) for assistance.

I would leave things alone and let them run their course because:

1. I don't know how or if you can cancel or rescind the W-7.

2. While you might be able to sneak an e-filed return through (assuming your original return is still in someone's in box and no action has been taken yet), I don't know what would happen next when the mailed return is attempted to be processed.

3. I don't know if you would even be able to e-file as a first timer with a new SSN.

The fact is, if you knew your wife was eligible for an SSN, you never should have filed in the first place, you should have waited and filed for an extension.  Now you're stuck waiting.

Also, after your tax return is processed and you get the ITIN letter, you need to send a letter to the IRS informing them of the SSN and you will only use the SSN going forward.  See this FAQ.

https://www.irs.gov/individuals/additional-itin-information