My wife was on Opt from Feb-2008 to sept 2008 and since oct-08 she is on h1b... while I am on h1b since 2 yrs... by mistake my wife's employer has deducted social security and medicare taxes(she being international student is not liable to pay this taxes).. in order to claim I have found out we need to file form 843 and 8316 as the employer is not able to refund it..
Now my question is like me being resident alien we would be filing married jointly 1040... I have come to known that if we file 1040 and then file 843 and 8316 IRS mit not refund the claimed taxes saying we files as resident alein.. and as resident alien we have to pay social security as well as Medicare taxes.. one of the tax experts have suggested that one of the way out in such situation is we take extension for filing taxes and meanwhile file 843 and 8316.. and when we get the refund we should file our annual return... kindly guide me into this matter..
Also if I file 843 after extension.. on line 6 of 843 I need to mention what form I filed for 2008 return.. if I mention that we have not filed and have got extension.. will it work?

If you file joint return as residents or if your wife filed resident return in 2007, she must pay FICA taxes.
The suggestion by "one of the tax experts" is evading taxes; so do not do that.
Read about F1/H1-B tax filing: Your U.S. Tax Return: The U.S. Visas

Mukata:

What the tax consultant suggested is NOT evading taxes, as the link below clearly shows she is NOT lable for FICA taxes even if she files jointly with her husband.

Nonresident Spouse Treated as a Resident

Hopefully, they followed the tax consultant's advice, because, once they filed jointly, that CANNOT be undone and it will be used as a reason to reject the Form 843 submission.