Get your taxes done using TurboTax

If you want to file separately you do not need an ITIN for your spouse.  You also don't need to come to the US to apply for an ITIN, if you want one. How do I get an Individual Tax Payer Identification Number.  If you do want to apply for an ITIN for your spouse, you will need to mail your tax return in with the ITIN application.  However, it's not required to be able to file your return using the MFS status.  

To file separately, just be sure that in the "My Info" section of the program that you have indicated that your spouse is a nonresident alien, but do not indicate that you want to treat her as an alien for tax purposes.  Ignore the messages in TurboTax indicating that the ITIN is missing and proceed to electronically file the return.