Your code is written so that the row is only incremented if your script tag is not found. However, it sounds like you want to unconditionally increment; if that's the case, then move $row++ to outside the if statement, like so:
if (!strstr($value, '<script>')){
$objPHPExcel->getActiveSheet()->setCellValueByColumnAndRow($col, $row, $value);
}
$row++;
If this isn't what you were looking for, then please provide a sample input that can be matched to the output, as this would make what you need crystal clear.