The new c'tan lore makes it apparent that the Emperor could never defeat a true c'tan. They were the living energy of the universe incarnate.
The shards are far less aware of their power, and thus less likely to realize they can incinerate continents with a quick snap of their metal fingers. Which in turn means they can be fought more easily by beings of similar power such as greater daemons or other powerful beings.
Regardless of McNeill's original intent, it's pretty clear now that even the Emperor could only have defeated a shard. Plus in an old WD article when the lore was first changed, Magladroth the Void Dragon is listed among those that were rendered into shards. None of them escaped the necrons' rebellion.
Nonsense is our Salvation