You've heard of crowd control, now check out how we do it in WH40K! We present to you Cassia, a walking WMD
Teenage mutant space princess being stronger than a tech priest magos and a literal space marine combat-wise is pretty funny. Although it might be lore-accurate, considering how rare and powerful the navigators are supposed to be.
In the lore Navigators are so rare and valuable that nobody would put in them harm's way except in the most dire of circumstances, so we don't know how strong they would be in combat.
They do have that warp-eye instakill thing, but I wouldn't expect most navigators to have extensive combat training.
Rogue Trader (both the pnp and this) takes a lot of Star Trek logic since there's very little reason to put your command staff in an away team rather than a specialized unit of house guard, battle psykers, tech priests, etc.