It's OK to shoot the "large" fragments. In fact, doing so will help keep the noobs from getting hit by them. It's when the large ones hit a ship that they break into "small" fragments which fly back and heal the entity. You MUST shoot the small ones on sight or else each one will heal 1 or 2% of the creature.
The CE doesn't start spawning the "large" fragments until it gets down to 35% health, and the small ones only come from the large ones impacting on ships.