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Solution: Install the extensions as described in the OP, and then just rename or remove ~/.jupyter/jupyter_nbconvert_config.json:

~/.jupyter$ mv jupyter_nbconvert_config.json old_jupyter_nbconvert_config.json

This file is generated when running :

jupyter nbextensions_configurator enable --user

and has the following content:

{
  "Exporter": {
    "template_path": [
      ".", 
      "/home/sschyman/Programs/sage-upgrade/local/lib/python2.7/site-packages/jupyter_contrib_nbextensions/templates"
    ], 
    "preprocessors": [
      "jupyter_contrib_nbextensions.nbconvert_support.CodeFoldingPreprocessor", 
      "jupyter_contrib_nbextensions.nbconvert_support.PyMarkdownPreprocessor"
    ]
  }, 
  "NbConvertApp": {
    "postprocessor_class": "jupyter_contrib_nbextensions.nbconvert_support.EmbedPostProcessor"
  }, 
  "version": 1
}

Not sure why it causes the error described, but deleting it does not seem to cause any harm and nbconvert runs as it should.