Never change content without the user’s specific manual request, and never ever delete anything from the DB that you haven’t created.
So the only question left is how to create you sample content. The cleanest way is to provide an exported sample that can be imported into WP. The only problem with this approach is that it requires the installation of the wordpress importer plugin. The other possible approach is to write a code that will generate the sample content, but this also needs to be triggered by a manual action by the user.
If your user is not very bright (as most users are 😉 ) you can show a short message about the existence of the option to import/generate a sample after theme’s activation.