The chances are that any background service, whether via MacPorts or not, is controlled via LaunchD, and there are just a couple of places that LaunchD looks for processes to manage.
Each process has a corresponding .plist file that tells launchd what, and how, to run - your fix should be as simple as finding this file and either unloading it (to shutdown the process) or removing it and rebooting (so that it doesn't load next time).
So look in /Library/LaunchDaemons for a file that corresponds to your Samba 3 process. The simple fix is to remove it and reboot, or you can:
sudo launchctl unload -w name.of.the.plist
(where name.of.the.plist is the name of the file you want to unload). The 'unload' tells launchd to kill the process, and the -w switch writes that change so that it's persistent across reboots.