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Django handles dependencies between models in migrations correctly. What it can’t handle, and what it explicitly warns against in the docs, is unmigrated apps with dependencies on migrated apps:
Be aware, however, that unmigrated apps cannot depend on migrated
apps, by the very nature of not having migrations. This means that it
is not generally possible to have an unmigrated app have a ForeignKey
or ManyToManyField to a migrated app; some cases may work, but it will
eventually fail.Warning
Even if things appear to work with unmigrated apps depending on
migrated apps, Django may not generate all the necessary foreign key
constraints!
In this specific case is seems that the registration app has a dependency on the user model. You need to upgrade this app to a version that has the necessary migration files to support Django 1.7+.