If a program would normally appear in Add/Remove Programs when installed, then it will appear in Add/Remove Programs when distributed through Altiris. It's possible that the installation method didn't provide for this. Windows looks at the registry for this data, in HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Uninstall
When you create a Software Resource, such as a Software Release, you can specify different command lines. I always specify Install - no UI and Uninstall - no UI for all packages, and supply others as needed. I suppose you could add only an Uninstall command line, such as if you didn't want them to have the ability to install the program, but only to remove it.
A background uninstall would use a command like msiexec.exe /x {GUID of program listed in the registry path above} /QN
A great resource for application packaging is AppDeploy.com. It's a little hard to search, in my opinion, but the information is valuable.
Does this help?