My preference, beyond crash damage being excluded from destruction until there is a better ship building/analysis UI, would be to have a ship repair suite. This would potentially be multiple machines (even multiple core sizes depending on the ship/parts). They could use scrap or materials/parts to fully repair a nearby/linked ship. Perhaps in this approach, cores/parts could be nanocrafter-repaired only three times or lose 10-20% efficiency each nanocrafter repair, before needing to be machine repaired.
I would prefer not to have mobile repair kits or anything requiring extra time to create. The current repair system of rushing back to a downed ship with nanocrafter/scrap and then using onboard scrap from repaired containers is already complex enough. My current ship takes 4.5hrs to repair with T1 scrap (done that three times before trying some T3 scrap). This has been more than enough punishment/cost for crashing each time - even with keeping container contents and ship.
It may be strictly realistic to have a ship/contents destroyed permanently on impact/crashing but, as a game, the current system is already a gut-wrenching enough experience. It may also be realistic to lose cargo or limp home but they add even more insult to injury. So, I think NQ should balance strict realism with enjoyable/challenging gameplay.
To introduce complexity into repairs for crashing, it may help to lock the ownership of a crashed core to the player for some time (eg 8/12/24 hours) to allow time to return from anywhere in the galaxy and repair (and create any complex repair items needed). I don't support the extra complexity but this could be a compromise approach if NQ was to go down that path.
For PVP, noting that it is consensual at the moment, I would be quite happy to immediately/completely lose any ships committed to PVP outside a safe zone. To encourage leaving the safe zone, the rewards should be much higher than in the safe zone (eg rarer ores).
Finally, it may be worth considering more intensive tutorials with flying tests to pass, even to unlock some talents/core/parts access. If someone has demonstrated the skills to fly a heavier ship, operate space engines or a warp core or even operate weapons, then these sorts of proposed damage/destruction limits could be easier to accept.