Obsolete the SOE
If you don't want to be forced to use an SOE, don't build desktop applications.
Secondly, don't build web applications that rely on anything that isn't a web standard. That includes anything that relies on a plugin, like Silverlight.
It occurs to me that if all enterprise applications were standards compliant web applications, the only thing an employee should ever need is an up to date browser. They shouldn't need an SOE. The IT setup process for a new employee should be:
- Give them a wad of cash to buy any machine they like
- Give them a login - ideally something that supports federation without actually needing to be joined to the network. OAuth or OpenID maybe?
- Give them the URL to your corporate portal
- Give them a network cable
If there's nothing to install on their system, there's nothing to be worried about when it comes to OS upgrades and messing with your precious SOE, since you won't have one. If the OS upgrade includes a new web browser, you shouldn't have a problem, since you used standards compliant HTML and CSS.