Correct inconsistencies between config file and website

These changes have no actual effect on the system. When a journal is
not integrated, the default values in the system (allow embargoes, use
blackout) override the settings in the config file. Here, I'm just changing
the config file to be consistent with the default behavior to reduce confusion.
Merge pull request #638 from ryscher/integration-2

Correct inconsistencies between config file and website