While there are things that could be done to try and hack this, I wouldn't recommend it. If you are including .Net Assemblies in your installation, Windows Installer actually talks to the framework when installing these, (for example, when installing to the Global Assembly Cache).
This means that .Net needs to be present before the Windows Installer package is launched--which is why InstallShield only exposes this as a 'Prerequisite' type option in the Release properties.
If you have the requirement to roll out .Net via SMS or AD or somesuch, I beleive .Net 1.1 is actually an MSI installation that you can extract from it's *.exe bootstrapper, although I've never tested this to see if the bootstrapper does anything special when it launches the package.