Microsoft\'s SmartScreen Filter under Windows 8 is a small developer\'s worst nightmare.
While I realize the benefits to end users and the effectiveness at stopping
Old question but I recently had the same issue where I needed to download a small installation package down to a user's pc for them to execute. But as always SmartScreen was blocking the download...
A workaround that I discovered is to package your installer file in a .zip (or the likes) and then have the user download this compressed file and execute the installer within. This is at least the "prettiest" solution that I had to use in my scenario.
This method saves you from having any kind of certificates assigned to your files. You just need your users to trust you, but this will bypass the SmartScreen Filter.
I hope this can be used as a workaround for your issue.