I've commited to cloud-init's trunk an improvement to cloud-init that works 
around this.
The fix there changes updating of .ssh/authorized_keys to update existing 
entries rather than appending.  In this case, then, the inserted key is 
re-written appropriately.

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https://bugs.launchpad.net/bugs/833499

Title:
  virt/disk.py unconditionally inserts  public_keys into
  /root/.ssh/authorized_keys

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