How to delete custom field “suggestions” from dropdown list

You can filter the query for these keys on'query'. I would start that filter as late as possible to avoid side effect.

Sample code, tested:

add_filter( 'postmeta_form_limit', 'wpse_73543_hide_meta_start' );

function wpse_73543_hide_meta_start( $num )
{
    add_filter( 'query', 'wpse_73543_hide_meta_filter' );

    return $num;
}

function wpse_73543_hide_meta_filter( $query )
{
    // Protect further queries.
    remove_filter( current_filter(), __FUNCTION__ );

    $forbidden = array ( 'the', 'keys', 'you', 'want', 'to', 'hide' );
    $where     = "WHERE meta_key NOT IN('" . join( "', '", $forbidden ) . "') ";
    $find      = "GROUP BY";
    $query     = str_replace( $find, "$where\n$find", $query );

    return $query;
}