drupal_mail() is formatting my body drupal_mail() is formatting my email body.
Before: http://pastebin.com/LbBy04BZ (note 1 line)
After: http://pastebin.com/nEx7AFwU (note multiple lines)

It should not, because Line 23 in /modules/system/system.mail.inc is the following one:

$message['body'] = implode("\n\n", $message['body']);


How can I prevent the reformatting of my mail content?
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;
}

//...
}