When I said Xcode 6 I really meant NOT Xcode 7. An Xcode 5 app was built a long time ago, and Apple have not allowed new submissions built with Xcode 5 for a long time.
I'm sure Apple originally said that San Fransisco would only be used in apps that were explicitly compiled with Xcode 7/iOS 9. In the past, similar functionality changes have been "opt in" based on using the new tools. So, in theory, an app built with a version of Xcode prior to 7 should behave as it always did, and get Helvetica. So, if you don't want to change anything in your app, the current app store version should "just work" on iOS 9. In theory! And if you do need to make some changes (perhaps to fix a problem that only appears on iOS 9), it should be possible to build with Xcode 6 (since you can't submit Xcode 5 builds anymore) without opting in to the new system font. Again, in theory...
I'm not entirely sure if this has changed during the betas, but I have recently noticed in beta 6 that an app I build using Xcode 6.4 and run on an iOS 9 device is getting a San Fransisco font when I use UIFont's systemFontOfSize method. But things like table views and navigation bar titles seem to be to be using Helvetica. This could just be a bug. Or maybe they really are going to force the new system font on old apps (which seems very aggressive) and developers have to make changes to ensure apps continue to work correctly on iOS 9 (whilst also supporting as many earlier versions of iOS as you deem necessary).
Sorry I couldn't be more help.