Of course they can. They own the directory server that hands out keys.
http://blog.cryptographyengineering.com/2013/06/can-apple-re...
tl;dr: Apple can send you a public key of Bob's new device. Apple can pretend to send you a public key of Bob's new device. And since it's proprietary software, they can trigger a resend of your recent messages to Bob.
Moreover, if you use iCloud backups, they have the keys to your kingdom, since it fails the 'mud puddle test':
http://arstechnica.com/security/2013/06/can-apple-read-your-...