Firstly, keeping your own backups of your sites' content is a very, very good idea. So we'd advise you to back up your content, because we make it easy: http://dhurl.org/22u
You have quite a few easy options to disable a site, so it depends on what you want showing. If you want nothing to load at all, you'll want to change your hosting to DNS-only (in your panel under Manage Domains > Web Hosting > Edit).
If you want to put up a simple "Coming Soon" or "Under Construction" page, you can do so with an index.html file in the site's directory.
Another simple option would be to have your site redirect to one of your other domains. More on that here: http://wiki.dreamhost.com/Redirect_Domain
And rest assured, setting your site to DNS-Only or a redirect will not wipe out your site's directory. But it's still smart to back up your content!
As I mentioned, there are quite a few other options as well, but these are probably the easiest. If you're looking for a different end result, please let me know, or submit a support ticket here: http://dhurl.org/dhsupport
Hope this helps!