Like Bainternet suggested – remove_meta_box( 'tagsdiv-custom_taxonomy_id', 'post', 'side' ); to remove the default Metabox. If you want to still see the terms. Then re-register the metabox with your own custom callback.
This callback function can then mimic the function used to display the default metabox – but simply omitting any input forms /checkboxes which send any data.
The function you’ll want to mimic is:
-
For non-hierarchical taxonomies: http://core.trac.wordpress.org/browser/tags/3.3/wp-admin/includes/meta-boxes.php#L265
-
For hierarchical taxonomies: http://core.trac.wordpress.org/browser/tags/3.3/wp-admin/includes/meta-boxes.php#L307
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