I don't know, I don't want letsencrypt to touch my config files. It just works fine without that "magic" anyway if you're willing to add a few lines to a config file.
If you use letsencrypt with "certonly --apache" (or --nginx, when the nginx plugin is released) it will make only transient changes to your config in order to obtain the cert, and then restore it to the original state before exiting.
If you use letsencrypt with "run" (which is the default command) it will make config changes if those appear to be necessary for installing the cert.
One challenge we've had is how to design the command line interface to ensure that the users who want maximum automation get it, and the users who want maximum manual control also get that. Both set of behaviour are available.