Unfortunately, SSO Upgrade wizard does not give you an option to modify the SSO deployment mode during the upgrade process. When you run the installer, it will automatically detect the SSO version and deployment mode installed on the machine and it will go ahead and upgrade SSO for you.
So to answer your question, if you want to change the deployment mode of SSO, you will have to uninstall SSO 5.1 and Install SSO 5.5 U2 with Standalone SSO mode.
That's what I assumed but I thought it was worth asking. Maybe I'll stick with multisite for 5.5 and then change when we go to 6.x.