I think most people did see that variation coming.
Really? Well, I said it first ;)
In a few of the novels it's mentioned (off camera) tha Navigators can get possessed, though it's a rare event. When it does happen though it's very very bad. If it happens whilst traversing the Immaterium the result can be ... unpleaseant. For this reason their are lots of failsafes in place.
The Warp Eye offers some protection, as does experience and skill (presumably Will Power). Some routes are inherently riskier than others, know thy limitations. The Geller Field of the ship offers lots of protection (whilst traversing the Warp). Each Navigator sits in a heavilly shielded cell (they can leave if not too mutated, but not whilst Navigating). Each Navigator undergoes intensive psycho-hypnotic conditioning to improve willpower and control and should cause an artificial allergic suicide if in danger of being possessed (this sometimes works, sometimes doesn't the Emperean is fickle and daemons tricksy). Finally, if all goes haywire each ship is geared to automatcally dump out of the Warp and into realspace in the event of the (guiding) Navigators death, something the Captain can do in some circumstances. The maneuover is very risky (it can happen or be induced in other circumstances too) but occassionally saves a ship, sometimes its crew. The results (location, timeframe, damage) are pretty random though.
Ship (and Navigators) are valuable and te Imperium goes to alot of trouble to preserve them when they can. Besides, after being rip-tided through the Emperean for a while, Hulks can be trouble.