Thank you for letting us know. Since Safari is a native application which can't be removed, we'd like for you to reinstall the iOS.
How to back up your iPhone, iPad, and iPod touch -- Please be certain you have a fresh backup to keep your personal information safe.
If you can't update or restore your iPhone, iPad, or iPod touch -- Even though the title of the article isn't specific to your issue, the section titled "Put your device in recovery mode and set it up again" will walk you through all the steps to reinstall the iOS on your device. Once your device returns to the Home screen, go back to Settings > Safari >Block Pop-ups to see if the issue is resolved.
Cheers!