I'm not sure if I understand the question, so I'm going to rephrase it first, but if I do, I have done a workaround for this.
Understanding the question as:
If the theme is deactivated, the site options are preserved so if activated again they don't need to be re-entered, but when deleted they are completely removed.
This is not a full answer because it speaks to the plugin deactivate versus uninstall hooks rather than theme, but assuming theme has something similar, what I did was this:
- On deactivate, I pushed the option settings into a small backup table.
- On activate, check to see if the backup table exists and if so, restore the option settings from the backup and drop the table (or just check for the row and delete the row). Make sure you name the table so it's clearly tied to the theme like the above notes on woocommerce. And always delete the settings after they're used so that you ensure the most recent settings are available.
- On delete, behave normally (which purges the option settings permanently).
This way the user doesn't have to redo the option settings if they have to deactivate to check for plugin and theme conflicts (as I recently had to do with a Woo theme).