drupal_mail() is formatting my body
Have a look at the API documentation for drupal_mail_system(), there you'll have code to override the default MailSystemInterface.

For an exemple of how to override it, have a look at the Postmark module.
You can then redefine the format() function:

class YourModuleMailSystem implements MailSystemInterface {

public function format(array $message) {
  //remove this formatting.
  //$message['body'] = implode("\n\n", $message['body']);
  return $message;
}

//...
}