I would recommend filing "Married Filing Separately" as your status. This way your financials are kept further apart, and you are each filing your own return. Because you were legally married for 2016, this is your best option in your situation.
To change your filing status in TurboTax Online:
1. Go to "Personal Info" at the top of the page
2. Select "Edit" next to marital status
3. Select you are "Married", then answer the question "Do you want to file this return together with your spouse?"
4. Answering "No" will get you the Married Filing Separately status
5. Continue answering the questions in this section until finished