According to Apple (see WWDC 2011 Session 510, In App Purchases for iOS and OS X, at the 48:55 mark), the only things you can do as a developer to prevent subscriptions from auto-renewing are:
- Raise the price.
- Remove the auto-renewing IAP product from iTunes connect.
In both cases, notification emails are sent to subscribers, though not immediately. The talk says Apple checks 10 days before a (yearly) subscription renewal and sends email at that time. It's not documented anywhere, though, so I'd treat that as an implementation detail.
I've done the latter (removing the product) several times with my own (monthly) apps, and it seems to work as advertised.
One important note: if your app is a Newsstand app, it must have at least one auto-renewing subscription available. If you remove the last one, the app will be removed form the App Store. Users who have already purchased it will still be able to use it, and will be able to download copies from the "previously purchased" section of the app store, but no new copies will show up for purchase in the App Store proper.