Make an silent install file by running setup -r.
This creates a responce file called setup.iss in your Windows system
directory. You can select the do not reboot option in the end of the setup
cycle. We have tested that the reboot is not necessary for the client to
work properly.
Run the silent install by running setup -s. Setup will look for the
setup.iss file in the directory from where you started the installation
process.

You also have to script the creation of the optionfile, like a normal
install.

This works fine at our shop.