Why not just turn off the default tags capability then register a tags taxonomy specific to the custom post type?
http://codex.wordpress.org/Function_Reference/register_taxonomy
register_taxonomy(
'my_custom_post_type_tags',
'my_custom_post_type',
array(
'label' => __( 'Tags' ),
'rewrite' => false,
'hierarchical' => false,
'capabilities' => array( 'edit_terms' => 'manage_categories' )
)
);