Married with immigrant

Hi, I got married in September and her visa is still active but her 6 months of being allowed in the US is expired, I’m in the process of getting her recisdency done but still have not submitted the paperwork. How should I file my taxes? The place I went to now said I cannot file married because she is here illegally since the 6 months are expired , do I file single? Can I file married? Could it affect the immigration process to say I have no been married since September? Thank you