I played against them last night, and utterly decimated them.
It really depends on his psychic dice, and how well they utlize the overly long Psychic phase they will have.
But you will have a strength because Thousand Sons tend to be reasonably low model count, unless they take Tzaangor hordes, in which case they lack in ranged weapons.
The Helm is by no means a waste because of how it also causes Perils if you successfully deny. Its not much, but its enough for your opponent to be wary and try to avoid it.
My suggestion is to just focus fire. Take Raiders loaded with Kabalites with guns, add Splinter Racks, and just focus fire on specific units until they're gone. If they take Magnus, take that sucker down with sustained fire, because thats going to be a MASSIVE chunk of their army points.