I would like something like this too. Make getting ships as difficult as you want, but don't take away my control by only letting my have whatever ships are for sale because everything else blows up (or suicides) every single time. Hauling in captured Hounds and scrap for hours on end is only fun if there's a point to it like getting a better ship. If all you can do with that money is buy/repair other ships you don't want either there's no point.
The crux of it is this: It should be quicker and easier to get the ship you want by continuous play. If I want a Hyperion, it should be easier to get by some in game means than by reloading a fight with it over and over until it is boardable. Making things more frequently salvageable at a higher cost would do that nicely. As it stands, it feels like there's no middle ground between self-imposed challenge of accepting that everything you want to pilot blows up, and cheating by reloads so that whatever you want is boardable.