|Well the other solution could be that the user installs a local piece of software, that in effect connects to a 'control' server and connects to the locally connected scanner. Then a separate web site 'could' send a message to the control server which then would tell the local software to act.
But note that whole interaction makes no sense, far to much of the process is the user interacting with the physical scanner. So controlling 'remotely' via web sites doesn't help the process at all.
Now if your actual concern is that the 'scanning, file, upload file to your site' etc process isn't as easy as it could be. Then yes I could understand that, but the solution would be a downloaded piece of software that interacts with all scanner types, scans and uploads the file to just your servers.
I think most people hitting this concern have decided its better to educate (via the websites) the users on how to do the process rather than solve it with software.