I am seeing that you can launch FaceTime from your app via
[[UIApplication sharedApplication] openURL:[NSURL URLWithString:@\"facetime://tel-number\"]];
As a general rule, if you use undocumented API calls and apple catches you, they will reject your application. The reason is because they could change the API call that you are using in new IOS updates and thus would cause your application to crash or not work properly. You can try and submit using the undocumented API and hope that apple lets it through but as i said, you run the risk of Apple changing this api call or removing it completely from the OS in the future.