Looking over the Navis Primer rules as they are written, I'm forced to concede that yes, they do make warp travel so hazardous that every trip is potentially as deadly to the group as a combat encounter. This is a long way from ideal, and so a less hazardous interpretation is probably required.
However- it's occurred to me that the danger level of the Navis Primer rules is exactly the right level of danger for a ship plying an uncharted route.
So, when I work out a less lethal method for PCs to use in any campaigns I run, I'll only use them for routes the PCs have a Chart for. There will likely be modifiers for the type of route- even with a Chart to work from, Haunted, Surly or Lightless should be dangerous trips (the Cape of Good Hope was charted, but still feared). At the other extreme, a Stable route with a Detailed Chart should be so safe that the travelling without a Navigator rules can be used casually- this, IMO, is how Chartist Captains work. Sticking to a handful of safe, stable routes that are very well mapped.
When the PCs decide to head out into the unknown and try for a system they've no chart for- that should defintely require the Navis Primer rules in full. A dangerous undertaking that uses up a significant chunk of game time is what this needs. If the route is a Surly or Lightless one? Well, that should explain why the background has people trying to steal or barter for precious charts of warp routes, rather than simply going out and mapping their own.
A quicker simpler version of the Warp Travel rules that doesn't give as much danger to starships is a very desirable thing, as long as it's used for travelling the beaten path. PCs should have a healthy caution regarding sending the ship off the charted routes, and not just do it on a whim.