Django Server inside another program
you have two options really. either run the app on the customer's hardware or your own. if you don't want your code exposed you should consider hosting the application yourself and providing them with authentication 
Django authentication is actually pretty robust, check out these two articles from the official docs. This is a general tutoria on authentication l: docs.djangoproject.com/en/2.0/topics/auth/customizing/… and this is a broader scope one on django in general docs.djangoproject.com/en/2.0/intro/tutorial01 
Edit: just do it here
I wrote a Django app that collects data from clients and displays them in it's web app.
Now I want to write a script/program (WPF or a small Java App) that manages the Django server. Things like Start/Stop, update Django files, migrate Data etc.
Reason is: I want to stuff all of that into an .exe, maybe with a setup and licensing for my potential customers.
What would be the most professional attempt to do this? I wrote smaller scripts before and built them with pyInstaller, which does not seem to work with Django. Or should I just install a python interpreter with my setup and just run the python files? Then my code would be visible to my customers.
Any tips are appreciated.