Hi boxcarpress,
I’ll think about the excluding.
About the settings thing: in short, this is a feature that is required for WordPress Network support.
In details: there are two setting in the db: one if for the actual, specific blog and one is global, that contains settings for all of the blogs in a network; both are obviously saved into the db, but the global config is “printed” into advanced-cache.php as well.
When the plugin is deactivated, the settings for current blog is removed from the global config and if no other site config remains, advanced-cache.php needs to be removed. This is why you might believe your settings are removed: if you’re using the plugin in a single-site layout, once you deactivate it, advanced-cache.php is removed and it needs to be saved again.
Also, I’m sorry, but I refuse to do this automatically, even though it’s possible; in my opinion firing up the cache without a supervision on the settings is not a good scenario.