Thank you for your question, I will try to answer as followed:
Will he get German passport?
--> yes, as the father is a German, but you will have to apply for that.
.Can we now do vaterschaft?
Yes, please contact the Jugendamt in your district and ask for Vaterschaftsanerkennung Process.
.Can they stop me from Ausbildung since I refused to do DNA test?
No, but please make sure you do start the process of Vaterschaftsanerkennung with the Jugendamt.
.Can they take my permit back
No, as long as you have the Ausbildung they cant.
However, I would consult auf lawyer on this case( there are probono Lawyers as well-depending on where you live).
Hope I could help.