Is the Apple AppStore still accepting apps that only run in scale mode in the new iPhone 6? Or do I need to adjust my whole app to be able to publish a new update?
Yes you can still submit apps as you normally would without adjusting your app for the newer screen sizes. It will auto scale for the iPhone 6 and iPhone 6 Plus (similarly to how the iPad scaling works for iPhone apps, but better). You should still test your app against these targets in Xcode 6 though. I've already found one scaling issue using GLKViews on the iPhone 6 Plus only. The contentScale factor is increased to 3 instead of 2 ONLY on the iPhone 6 Plus. I will also note that it seems you must still take screen shots for all screen sizes when submitting your app to the app store. So regardless, you must run on all device sizes.