If you take a closer look at the ConfigureIIs custom action in the InstallExecuteSequence using Orca, you'll see its execution depends on the property called SKIPCONFIGUREIIS. It is "all-or-nothing" switch, and if you set this property for those cases when your IIS-related feature is off, the installation won't try to address IIS services.
Hope this helps.
Yan Sklyarenko
2010-10-27 06:45:35