My first recommendation: Don’t do it!
If the plug-in author releases an update, you can and will run into conflicts. Particularly if someone installs both the new plugin and your theme at the same time. A much safer route is to build plugin support into your theme. Make things degrade gracefully in case the plugin doesn’t exists, but don’t actually code the plugin into your theme.
If you’re still intent on hard-coding things …
Put the entire plugin in a subfolder for your theme. Then, from your theme, call activate_plugin() to turn the plugin on.