Changing the Navigation alias for Home breaks the entire site, granted this can be fixed in the backend using SQL... but this does not appear to be acceptable behavior.
It is also possible that changing other 'default installed' aliases (Root, Home, Utility, Images, Files, and Trash) will break the site, however I have not tested this.
I think there are at least two possible solutions to this problem:
1) Do not allow the user to change aliases for the given navigation items as changing them breaks the site.
2) Do not rely on a hardcoded alias as the user could change it to any value.
Windows 2003, MS SQL 2005, Coldfusion 8