In Xcode, click on your project, then your target, then scroll down the summary and check off "Use Entitlements" and "Enable App Sandboxing". Does your app still work? Then you should be fine. I suspect your app doesn't work within the sandbox though, and so there's no way to submit such an app.
You can, however, sign it as a developer and distribute it some way besides the app store. Or just distribute it without the app store and skip signing it altogether, although non-savvy users wouldn't know how to install it, and what use does a savvy user have for such an application?