Really, I think putting this into the game in the first place is the problem. If astrogation is meant to be a non-trap or non-emergency option in the game world, it should not have a random chance of wiping the ship. Doing this means that you're forcing a PC to have this skill if you want to engage with the system.
If you want to be old-school, be old-school. Why not look at actual historic voyages, and make the check to successfuly make it through your hyperspace-du-jour a series of checks, requiring expertise from multiple non-exclusive skill sets, so that making it through the void is inherently something you need a crew (or party!) of skilled, highly-risk-tolerant experts for?
If you expect a game to include both social courtly ballroom drama, back-alley knife fights, and heavy-weapon battlefield combat, then you need to make sure that if you have the Diplomat, Shiv Artist, and Tank Jockey classes, that all of those classes can at least contribute in their non-specialist encounters, unless you want your players to be bored when they're not in the one type of situation their class is good at. And likewise, if you want to make astrogation a challenge which can wipe the party, then you should damn well include a good amount of mechanics to let all of your expected character types engage with it. Include steps like hull inspection and delicate micro-maneuvers in nullspace and the sheer grit to will yourself upright and conscious to make it to the emergency stop control when you hit a nerve-flaying warp storm, to turn what would have been a lost vessel into a badly off-course one (and one badly-fried PC who made the effort).