You can indicate an alternative directory for templates to be run outside of the normal [cfusionmx_home]\wwwroot. All you need to do is edit [cfusionmx_home]\wwwroot\WEB-INF\jrun-web.xml and add a <virtual-mapping> entry (within the <jrun-web-app> entry) for each directory designation:
Where “alias” is a virtual directory name you'd now use in URLs to point to code in “realdir” directory as: http://[yourserver]/alias/template.cfm
Be sure to restart the server after making any such changes.
You'll notice that there are some entries already there for creating the default mappings.