After seeing some of the problems that Microsoft has had upgrading people from Internet Explorer 6 and also seeing how Firefox has automatic updates, it\'s made me consider the
If I have it straight: Some users will go to a website to use your system while others will download a binary?
In that case, I'd force the download folks to upgrade. What if you make a change to the underlying database that effects how the client interacts with it? It'd be a pain to write every new version to work with those stubborn people using version 0.1 when you're already on version 4.0.
I'm assuming the web app and the downloaded binaries are using the same database. If you have a setup where an organization maintains it's own database, definitely do not force updates.