How to delete Instances in Amazon EC2 ? Change Pair Key?
Give it some time. Deletion of terminated instances is not a high priority task within the EC2 stack (seems reasonable to me). Eventually the terminated instance will drop out of the interface.
If your instance uses the instance store as its root device (e.g. it's not an EBS backed instance), simply terminating it will destroy the instance and you won't have to do anything else.