there's no way to tell what's safe, and what's not, therefore
   it's best to just leave it out.

That's not quite true.

One approach would be to install two copies of the config files... one
in "/etc" and another in (say) "/etc/.stock".  If /etc/foo and
/etc/.stock/foo are bit-for-bit identical, you can just install the
new one without asking; otherwise, you do a three-way merge (under
human supervision, of course) using "diff" and "patch" at install
time, failing if there are any .rej files.

During the start of the install phase, you install the "new" config
files in /etc/.nstock; once the merge is successful, you move that to
/etc/.stock

				- Bill




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