In order to use an application packaged with ThinApp, all you need access to is the package. This gives you unique flexibility. There are many ways to provide access to the package. You can store it on a USB key and give the USB key to your user. You can use Dropbox or any other file sharing method to distribute the packages to the end users. I'm not saying you should throw out any existing deployment tool you may have in place. But you should consider using alternative methods if you don't have an effective method of managing applications today. Let's say you have to deploy an application to a couple of contractors. Simply create a Dropbox share, put the application package on the share, invite all the contractors and you're done! No deployment tool agent needs to be installed on the contractors' machines and so you have not altered the contractors' machines in any way.
If you place your package on a USB key, you have your application with you anywhere...