Update
according to Harrison's comment, this should be
c.NotebookApp.tornado_settings = {'headers': {'X-Frame-Options': 'ALLOW-FROM https://example.com/'}}
now, see also http://jupyter-notebook.readthedocs.io/en/stable/config.html
Original publication
Ok, I found a solution that works, but I'm not 100% sure if this is the right way to do it: In .ipython / your_profile / ipython_notebook_config.py add
c.NotebookApp.webapp_settings = {'headers': {'X-Frame-Options': 'ALLOW-FROM https://example.com/'}}
Works for me, but not sure if this overrides more settings from a tornado or something else :)
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