Welcome to the Wefugees Community and thank you for sharing your situation with us.
In general, rejected asylum seekers are allowed to marry in Germany (we discussed a similar question here, for instance). Of course you could also marry in church. However, the marriage in church is not the official one (recognised be the authorites) and you would still need to register your marriage with the registry office (Standesamt). The Standesamt is most probably requesting a number of documents, i.e. a passport, a birth certificate and a proof that you are not married already. Please see also our blog on this topic.
I hope this helps and please don't hesitate to get back to us with any further questions.
All the best,