In my twenty years here, I've never seen filing as single be an issue in the visa process. Many do exactly that, then amend their return after their spouse arrives and is assigned a Social Security number. In reality, NVC won't care at all, and the Consular Officer doesn't either. Just have your spouse explain, they don't have an SS number and you'll amend the returns after she arrives. Works every time it is tried. Unless you are an IRS employee, this is a non-issue, and if you were, you would have done it correctly.
For rank and file taxpayers, there is no penalty for overpayment of taxes. That's the result of your filing choice. A later choice to amend, will cancel out the overpayment.