I love the extension, and would really like to see this feature implemented (save tabs automatically on window close, but remove them if closed individually). I poked around the api for google chrome extensions and found this, the last flag looks like exactly what you need.
onRemoved
chrome.tabs.onRemoved.addListener(function(integer tabId, object removeInfo) {...});
Fired when a tab is closed. Note: A listener can be registered for this event without requesting the 'tabs' permission in the manifest.
Listener Parameters