Since software defined networking is mainly controlled through applications instead of ports, that's where industry-watchers expect network engineers to be doing more of their interaction with the network in the future, not through the command-line interface.
Does that mean that the CLI will eventually be dead to the network engineer? Does this mean that many network engineer jobs will dissolve? Those are the big questions debated in this article at NetworkWorld.
I'm personally more inclined to agree with the F5 architect, Alan Mimms, who says that network engineers will still need the CLI to diagnose and fix problems that come up after access control lists have been configured, for example. It's the Garner analyst in this story that seems to think that SDN "if done properly" will obviate the CLI.