One last time for anyone whom missed the context (they exist...):
SBP act like the immature character he is, disrespecting two members of the Legion:
That pisses off Mordru whom decide to "put him in his place" AKA magically slapping him in the face, as Wizards aren't prone to physical confrontation:
There is not a single indication of Mordru wanting to kill Superboy Prime, even the spell he uses his weak, showing a sign of anger but no attempt to kill SBP.
In short, Mordru used a weak spell to correct SBP.
That's similar to Ares making a speech to the Dark Avengers and Bullseye trying to play the smartass.
He pissed off Ares and received a big slap in the face.
So one more time:
SBP isn't immune to magical attacks.
He lacks Superman's vulnerability to magic which means that he endures the attacks with his normal level of invulnerability.