There's a difference between your Facebook Application and your Facebook Page. Your Application is just for your website to allow for social authenitcation or to show your site within the canvas area that you posted in your image above. The Facebook Page is separate from your App and a destination for users to find out more about your company within Facebook.
Disabling the Social Discovery option within your App should not affect your Facebook Page at all.
I hope that helps, but if not, or you have other issues, just let me know.
Thanks,
Alex