Sure, I guess? Some semblance of balance still needs to be present if you want any sort of longevity, even if it is singleplayer only, saying just don't use him is a bit silly since he's the bloody faction leader, not playing him the way he's been designed to be played is gimping yourself intentionally because the devs were too lazy to balance things properly. The old Beastmen were too weak, and I get wanting to buff them but I think they overshot a touch.
Because it's not just Malagor, tho he's the most glaring example, any bray shaman with the beast lore can do almost as much horrible things to any infantry heavy army. I'm not sure if traitor-kin was this stupid before but it's essentially a flock of doom except better.
No idea if you can view the actual numbers for both skills anywhere, but from what I've seen in combat, flock of doom has a high chance of affecting the target but it deals fairly low damage over a short period of time, so you generally need at least 3 casts on a healthy unit to see any models going down, even if the entire unit is stuck at a third of their max hp. Traitor-kin on the other hand seems to do stupid high damage but has a lower chance of actually hitting, I've seen it start racking up kills on the first cast, and this was fairly significant numbers of dead units, only to see it fall off as their numbers got reduced.
And as nenjin pointed out above, it's not just that he's bonkers strong, the big part of the issue is that unlike cheese and doomstacks other races get, Malagor gets to roll over shit after a few turns only since you only really need to upgrade flock of doom itself and then rush the first cost reduction skill.