May I choose a planet to attack in an opposing system where I already have tokens?
You played this correctly.

The only rule explicitly stating that the offense gets to change their Destiny card is when they draw their own system. The rule book is also explicit that the defending player must still defend, but with 0 ships (on page 12): 


  As stated earlier, if a player has no colony on a home planet that he or she is defending, the player defends the planet normally except that his or her ship count is zero.


This section covers your problem. The offense drew a system where the defense had no colonies, so the offense picks a planet and attacks normally. The player whose home system is being attacked still gets to defend, but with 0 ships.