If it is a decision of BAMF, it is really unusual. For what country have you got a deportation ban? For Greece of for Pakistan? Or for both? I would expect a deportation ban to Greece from a number of the courts in Germany, but not from BAMF in the first place. Probably your decider took into account that the situation in Greece is counted to be very bad for asylum seekers and naturally for the rejected asylum seekers too, giving you protection against the deportation to Greece because of the possibility of violation of European Human Right Convention in this case. As you are married to a German woman, it is also possible that it was a reason too, because the separation of the family ist also against the European rules and against the German Basic Law (Grundgesetz). It could be a reason for a ban against Pakistan but it would be very unusual. Anyway you are lucky.
In the same time your asylum application is rejected as inadmissible. It is a question if you can proceed against it (if you still have time, it depends on the time frame for the appeal). But here you really need a good advice from an expert who will read the whole decision with all the reasons. With a depotation ban only you normally can apply for a residence permit after §25.3 Aliens law. In most cases people get it, but sometimes they only get Duldung at first, because the Ausländerbehörde has some discretionary power in this case.
As you are a husband of a German woman, perhaps you can take another way. Your lawyer can check if you have a possibility to apply for a residence permit after §28 Aliens law (for family reasons, family union with a German). Normally you must make a family reunion going to your country and making a visa procedure, but with a deportation ban it must be possible to get it in Germany. Anyway with the ban against Pakistan. With the ban only against Greece - I am not sure. Ask your lawyer.