If the client is an .msi package, you can do this by using the 'Installed Software' tab in the Computer Explorer.
First, in the EminentWare console, browse to a machine with the ISA client installed. Second, launch the Computer Explorer on that machine and hit the 'Installed Software' tab. (Note that will install the EminentWare WMI provider on the machine, if it's not already installed.) Third, from the list of installed software, select the ISA client, and use the 'Uninstall Software' button in the upper right corner of the Computer Explorer. Verify that the selected software shows up in the dialog, and hit the 'Uninstall' button at the bottom of the dialog. You will be taken to the Task Options Wizard, which will have the current machine selected. From here, you can add computers, WSUS computer groups, entire OUs, or even the entire domain to the task. Finally, hit next to enter your scheduling, export, and email options, and click 'Finish.'
Let us know if you have any issues.