Welcome back to the Wefugees Community and thank you for reaching out to us again.
First of all, I am sorry to hear that you are in a stressful situation. I would highly recommend you to get some individual support in a migration counselling office! It is hardly possible to assess here whether you are at risk for deportation or not - especially without knowing your background in detail. In general, people may be deported when they are obliged to leave the country under an enforceable decision but do not leave voluntaritly within the given period. This only applies, though, if your deportation is actually possible and not prohibited for legal reasons. If you were issued the Duldung because your idenity is not clear, the Duldung may not be extended or even revoked as soon as you hold a passport, for instance. Then, you can get deported in principle.
You are not living together with your spouse? In general, you may be able to apply for a residency permit card for family members of nationals of EU member states - one of the requirements is, however, that you are "cohabiting as a family with a citizen of the EU". It might be difficult to convince the authorities of your bond when you don't live together. Is your marriage registered/recognized in Germany? Why did your spouse not inform the immigration office about the marriage? Of course you need to submit the respective documents at the immigration office and actually apply for a residence permit as well - they won't issue anything without a formal application.
Please let us know if you need support in finding a respective counselling office in your area and don't hesitate to get back to us on your case or with any further questions.
All the best,