Add "Clean install" checkbox with appropriate warnings and option to back up styles and tab history where the user can specify and/or change the suggested backup location by default. Offer an easy option (inside menu?) to restore from the backup once installed. Take a look at Visual Studio editor options can be exported (backed up to a file) and subsequently restored later.

Also, take a look at nVidia, AMD Radeon (formerly ATI) and perhaps Intel network card driver installers as an example for "clean install".