acf's delete_sub_field call http://support.advancedcustomfields.com/forums/topic/remove-sub_field/ only makes the value null it doesn't actually delete the row. This does.

remove-acf-repeater-row.php

<?php
/*
*  deleteSubField
*
*  This function will delete a value of a sub field entirely and replace the rows correctly. 
*  ACF's built in delete_sub_field only sets the value to null
*
*  @param	$field_key (string) the field key of the top level custom field
*  @param	$repeater_key (string) the field key of the repeater element
*  @param	$post_id (int) the post_id of which the repeater is stored in
*  @param	$repeater_obj (mixed) the value of the row to be deleted from the repeater
*  @param	$field_name (string) the name of the field in the repeater to be searched on
*  @return	(boolean)
*/

function deleteSubField( $post_id, $field_key, $repeater_key, $field_name, $repeater_obj ) {
  $value = get_field( $field_key, $post_id );
  $pos = 1;
  $repeater_position = null;
  // Loop through the repeater to find the position of the correct row
  foreach($value as $key=>$field)
  {
    if($field[$field_name] === $repeater_obj)
    {
      unset($value[$key]);
      $repeater_position = $pos;
    }
    $pos++;
  }
  if ($repeater_position == null)
  {
    // Value not found
    return false;
  }
  for( $i = $repeater_position; $i < count($value); $i++)
  {
    // Move each item in the array back one, starting at the position of the repeater
    update_sub_field( array($field_key, $i, $repeater_key), $value[$i + 1], $post_id);
  }
  // Now that each element has been moved back one, delete the last repeater item
  delete_sub_field( array($field_key, count($value) + 1, $repeater_key), $post_id);
  // Update repeater value with new length which will remove the last row
  update_field( $field_key, $value, $post_id);
  return true;
}