Oke, figured it out after a good nights sleep.
I added a /css/ folder to my themes folder. As it seems, the /css/ folder will also be deployed, adding or overwriting the default content of the folder as is created when running the application. So I added my login.css to the /css/ folder in my theme and after deploying, the login.css that was created by default has been overridden with my css file sing the same name.