Thanks for the report. This is by design, currently, but I’ll open an issue to reconsider that design.
The default setting is not to use Pro. When you deactivate the plugin, it cleans up after itself in the WordPress database, which includes removing its settings in the database.
Would your preference be that a plugin like this leave a permanent trace of its previous settings in your WordPress db? (Trade-off: you wouldn’t have an easy way to clean it up later if you actually wanted to remove such orphaned data.)
Or would you prefer that the settings be retained “for a while” before automatically being cleaned up? (This would allow you do enable/disable within that window of time and it would remember its settings, but it would also eventually clean up after itself–and only then “forget” those prior settings.)
Or something else?