Dear @Idowu,
Welcome back to the Wefugees Community and thank you for reaching out to us again.
In general, marriages conducted abroad can be registered in Germany as well. Please see, for instance, this thread and the websites mentioned there for more information.
However, please be aware that as long as you are in the asylum procedure or your application got rejected (and you are holding i.e. a "Duldung" now), it would be hardly possible to leave or better to say to re-enter Germany legally.
As recognized refugee or holding a temporary residence permit (i.e. after getting granted Subsidiary Protection) you are allowed to travel within the Schengen area for up to 90 days within a period of 180 days without a visa though.
For the requirements to obtain a residence permit as spouse (family member) of an EU citizen you may check this website of the authorities in Berlin.
I hope this helps and please don't hesitate to get back to us with any futher questions.
All the best,
Meike