I've created silent installs. I have not looked at the Secure Desktop install package. However, the Sametime installation is contained in an archive that can be opened with Winzip. The unarchived installation files were created with InstallShield. You can create a silent install with any InstallShield package. Check here.
You'll also want to check InstallShield's site.
You can generate an answer file for any InstallShield package by executing the setup.exe file in the UI with a command line parameter. It will track your dialog choices and spit out the answer file.
Here's an example of one for Sametime 2.5
szDir=C:\Program Files\Lotus\Sametime Client\
Check the first site I gave you. for some good instructions and examples. It will tell you how to generate the answer file as well as how to execute installs, and uninstalls, silently.
If the Secure Desktop is also an InstallShield package, you should be able to do the same.
You can tell your SMS Admin to stop being lazy and do this for you.