Accidentally filed jointly instead of MFS

Hi Everyone, 

So I accidentally filed for a joint return rather than a MFS. My wife’s parents are trying to claim her this year. We eloped and we don’t want them to find out that we got married.

I already sent my 1040x to grt it amended. I was just wondering if I did that, will it take her SSN off the system so they can claim her? 
Thank you.