The (soon to be beta) release of MapGuide Open Source 2.2 will include an even more flexible installation experience.
In addition to configurable IIS web sites, you also get:
Configurable port numbers
Configurable virtual directory name and web server port (for Apache)
Configurable virtual directory name for IIS
All these changes ultimately make it easier to install 2.2 alongside an existing 2.1 or earlier release, by making the common points of conflict all configurable.
Side-by-side installation is not a supported scenario, but at least these changes will make it easier for you should you choose to take that path.