Isn't there just some registry key that can be pushed out or updated when installing a newer version of CAD software rather than having the end user who may or may not have permissions to re integrate ProjectWise Explorer client through the control panel?

When installing a newer or updated version of CAD software Projectwise will look for and update registry keys on the client machine, but it all depends upon what you are installing and what version of software it is.

You can use Microsoft installer technology to include ProjectWise (see) http://communities.bentley.com/products/projectwise/content_management/w/wiki/5497.aspx

Keep in mind, if it is AutoCAD you may also have to install a new add on module, dependent upon what version you are using.