Well one thing is for sure: Don't try to kill him. There might be a small chance to kill him if he is on the ground but as soon as he is flying you shouldn't even try.
Mathhammer tells us that even a BS5 Ghostkeel Wing with VT would need 2 whole shooting phases to take a single wound off of him if he's pushed himself to a 3++ (which is fairly easy). Totally not worth it at all.
So the only thing that's left would be to focus on the rest of his army and play the mission. TSons are fairly expensive and with a Magnus on the field he can't have much else at 1k points so that should be pretty easy. Small Plasma Crisis teams to kill stuff and Kroot MSU units to get all the objectives before Magnus can kill each of them would be my way to go I guess.
Some durable stuff sounds good to me as well. Especially the Ghostkeel. But without knowing what Psychic Powers he will have it's hard to say imo.
And last but not least....bringing Magnus to a 1k point game sounds like as much a dick move as bringing a Riptide Wing or a Stormsurge.