Im not sure it was "Targon" as a whole that decided the Darkin should be... punished. But rather the Aspect of Twilight working on its own judgement, and yes I know Pantheon was involved but there's no specific lore to say he did so for any reason other than to be involved in the biggest conflict of the age. But I could be wrong on this entire thought. I am curious however if The Protector would have been for or against what happened to the Darkin faction?
Anyway.
The Aspect of Twilight's punishment for the Darkin was to exterminate them, and on the whole that is what happened. However it wasn't done directly by Targon but rather the Shurimans who were taught how to trap a handful of extremely powerful Darkin and use those weapons as an advantage over the rest. I think Twilight went to this trouble because it would be poetic justice to have the God-warriors killed by mortal beings.