On J1 as research scholar your husband was exempt for 2-years from FICA taxes as well federal income tax.
In 2007, he must file resident tax return. So you will need to amend your tax return: File 1040X, with properly done resident return.
You claimed standard deduction on 1040NR, which is not available to the residents. Also on 1040NR, you cannot claim spouse as dependent. So chances are high that you will get a letter from IRS about your tax return with an additional tax bill.
Only F1 and J1 students can claim standard deduction and exemption for their spouse. It is not available to research scholars.
For the U.S. and India Tax treaty, read:
Your U.S. Tax Return: U.S. Tax Treaties for Students and Apprentices