Yes, you can kill Dustia again. You'll need to leave the Westersand though. Return to Rabanastre (you might want to save and restart while you're there, just for good measure, I'm not sure it it's required), and then when you return to the Westersand, you should be able to make Dustia appear again.

There are some Rare Game that will disappear forever after you kill them, but Dustia is NOT one of them.