I am sorry to hear, you are unhappy.
The app does not contain any changes for theme, neither for default templates. On your screenshot, you can see that the app updates FX Pages Docs Listing template (a black line above the files). This template should be indeed updated if you would like to use new features from FX Pages 2.0.
In FX Pages 2.0 you have a setting that allows you to change the pages where sidebar will swap the position.
If you do not choose any page here, your sidebar will not be touched.
Yes, indeed. All these template bits have been changed in FX Pages 2.0. These changes apply to all templates, starting with FX Pages... However, there are no changes for default templates, delivered by IPS right after installation.
If you have not accepted anything, then nothing can be broken, as no changes to templates have been made. If you have accepted the changes and something got broken, then please a bit more information to it.
If you are not sure how to update, then:
uninstall the app System->Site Features->Application
delete all templates that start with FX Pages ... from Pages->Page Management->Templates (be sure to remove block and page templates as well!)
delete menu block in Pages->Page Management->Blocks
delete the database page in Pages->Page Management->Page
install FX Pages again from Marketplace, follow the video tutorial to setup it from scratch.