Personally I always remove the default vhost that comes with debian from the sites-enabled directory. I also replace the apache.conf with something that is sensible for our environment.
Those a are config files and dpkg (backend to apt-get) should expect them to be changed. Tools like puppet run apt-get in a way that will keep the "old config" in case a package updates it's configuration, and if you run apt-get interactively it will ask you what to do if it detects a change in the configuration files.
That is any change not just a conflict that can't be merged automagically. After all even if it could be merged it could yield some configuration you don't really want in your system.
To break of a flamewar (sorry, that should really be discussed elsewhere but I just need to say it): My opinion is that even upon installing a daemon it must not be started automatically. For any decent site the default config is almost always wrong. (Yes I know that I can set dpkg options so that it won't be started, I'd rather like it to be the default)