The fourth argument for the toArray() method tells PHPExcel whether to do that or not
/**
* Create array from worksheet
*
* @param mixed $nullValue Value returned in the array entry if a cell doesn't exist
* @param boolean $calculateFormulas Should formulas be calculated?
* @param boolean $formatData Should formatting be applied to cell values?
* @param boolean $returnCellRef False - Return a simple array of rows and columns indexed by number counting from zero
* True - Return rows and columns indexed by their actual row and column IDs
* @return array
*/
public function toArray($nullValue = null, $calculateFormulas = true, $formatData = true, $returnCellRef = false) {