Zimbra is a mail server and it has a web interface. So if you want or need to use it you'll have to expect it to run somewhere. While I agree we should make it easier to work with your current web server/DB it's not our first priority. Our first priority is to make it very easy to install as a stand-alone collaboration server. Of course since our code and installer is open source if you *really* don't like it you have the freedom to just fix it.
That said in the future we'll be providing ways to make the install more flexible for those of you who want to run in a mixed or shared server.
If you just want your mail to get forwarded to Zimbra you can use fecthmail to pull your mail or you can just have your current MTA route mail to Zimbra. Both of these will allow you to store, index, search, etc all your mail and access it via the web interface.