Your wife is currently exempt from FICA (Social Security and Medicare) taxes. you can download IRS Pub 519 from Internal Revenue Service and print out pages 50-51 to show her employer.
With those pages from IRS Pub 519 in hand, she should go to her employer and politely ask tha they refund the improperly-withheld FICA taxes for 2009 and STOP withholding these taxes until her F-1 visa expires.
Her FICA tax exemption is good EVEN IF she files jointly with you. This is clearly shown at the IRS link below:
Nonresident Spouse Treated as a Resident
If the employer refuses to refund the FICA taxes (which MAY happen even though the employer gets a refund as well), then she must submit Form 843 and 8316 to request the refund direct from the IRS.
However, all this MUST be done BEFORE you file jointly, because, once the joint filing is done, the IRS will NOT honor any FICA tax refund request via Form 843.