There is a downloadable tool from InstallShield which modifies the manifest of a built setup.exe or update.exe. At this point I don't recall which versions of InstallShield's output it works with. It will remove digital signatures as it modifies the contents of the .exe file.
http://support.installshield.com/kb/view.asp?articleid=Q113245
(As a disclaimer I am paid to work on the product. I still recommend instead using a version of InstallShield which offers the option to select a manifest. I believe that's InstallShield 12 for MSI setup.exe, and something later such as InstallShield 2010 or InstallShield 2011 for InstallScript setup.exe and MSI update.exe files.)