Apple are perfectly happy with the second hand market for iPhones.
I've just ordered a 5S. It's costing me £709. My iPhone 4S 64Gb is worth about £200 second hand. Even a new 8Gb 4S, the cheapest model available new, is £349.
Anyone interested in my second hand phone was almost certainly never going to spring for a new iPhone.
The market for second hand iPhones does next to nothing to cannibalise the market for new iPhones (which Apple cares about) and strengthens the iOS ecosystem (both by bringing in new customers who might buy apps, music and movies but also keeping customers away from competing platforms).
There's more upside than downside for Apple in second hand iPhones.