Can't disable module when it defines an field type used by a custom entity
So as Clive suggested I solved this by creating a helper module called emtr_fields.

The emtr_fields module creates the entity and has the field schema.

Then the main emtr module creates the field and it's instance.

To remove all of this again first the emtr module has to be disable AND uninstalled (it has to be uninstalled as the field and it's instance is deleted in hook_uninstall), and then the emtr_field module can be disabled and uninstalled.

I also found some documentation on this on drupal.org here:

Module cannot be disabled because Drupal claim "Field type(s) in use"

Moving field(s) definitions into a separate module of a installed module.

Field types should be defined by one module and implemented by a separate module.