I agree that the player should have more control over ship restoration. The high base cost as well as it being all-or-nothing is something I've found contrived and un-immersive.
There are two potential issues I see with the change. Since there are upsides to d-mods, it could incentivize some weird strategies, like getting your ship blown up deliberately grinding for the right d-mods. Now, if there where hullmods that had a similar effect to d-mods, and if unspent OP reduced maintenance, there would be no incentive to make d-mods happen. Suppose you don't like the increased gas usage of using your car AC. Then you wouldn't just shoot at it until it broke. You just wouldn't turn it on, or would uninstall it. So hullmods for stripping ships down to essentials should be the better economy option.
The second issue I see, is that it could 'un-gamify' the early-game process of buying the ship that has the least ill-fitting d-mods. Which is something I've found interesting. When you can't pick and choose, and all you can get are beaten-up freighters and pirate ships, then you have to pick the hull where the d-mods don't degrade the attributes that are crucial for that kind of ship. And having fine-grained control over restoration would lessen the impact of that choice.
However, at that point in the game, you're also low on credits, and needing the ship right then and there. So the cost penalty for restoration would preserve some impact of the purchasing choice. I think having the restoration take time would be an interesting mechanic. With each removed d-mod taking several weeks, and then having the ship delivered, like with the arms-dealer delivery. So buying some pirate wolf with a glitched sensor array, and just keeping it that way, would make sense if you're broke and in a hurry.
Planets having varying capabilities of restoring hulls would be pretty neat too, if the difference could be both conveyed and reasonably predicted. So it would be worthwhile taking a d-modded Aurora to Culann for restoration, rather than to some backwater, Culann knowing the blueprint and having high ship quality bonus giving a significant improvement to cost and speed of restoration.