Yes. If she is earning income WHILE in the US, and you do not file a joint return, she would need to file a 1040NR to report the income that she earned while living here. Since she is working online based out of the US, this would be considered US sourced income. In this case, she would only report the income while actually in the US that she earned, not the income while living in her home country.
TurboTax does not support the 1040NR, but our partner Sprintax.com does.
The biggest difference in filing jointly or separately will be her counting her income while she was not here versus counting all her income for the entire year.
Also, something to consider is that if you file separately, there are some credits you are no eligible for so it is possible that your tax liability will be higher. You can do a return with and without her (BUT DO NOT FILE BOTH) to see what position it puts you in.
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