The problem with trying to get the game to police illegal destruction, is first and foremost the actual acceptance of mindless toxic destruction itself. How does it makes sense to in anyway reward/tolerate a player destroying another player (who most likely isn't interested in PvP, let alone outfitted for it) for no in game reason. And the more one sided and pointless the combat, the better.... And if a Wing of you can do it it fully engineered combat ships, against someone without even a weapon fitter? All the better!
The whole point of the OP is eliminate the concept of "outfitting for PvP". It also heavily mitigates the single-fight-performance-impact of fitting for combat in general. No matter what you fit for, you can still mount a full defense, and you can still carry a full rack of weapons. Even a ship stuffed to the gills with cargo holds could still max out the hull defense of their ship, and max out the shield defense of their ship just by taking a full sized shield generator. Engineering would no longer provide a huge stat increase either (just specialization), so even a vanilla ship could mount a respectable defense vs. an engineered attacker, without needing to give up internal module space. Ships smaller than their attacker could run away, since they'd be faster. Furthermore, cops would actually be relevant again (since they'd be comparably powerful to player ships).
The OP is all about eliminating the incredibly asymmetrical combat situations that gankers thrive on. With those changes, it would be significantly more difficult to find "easy kills", and significantly more difficult to illegally kill more than a handful before the getting your butt (as well as a steep rebuy) handed to you by the cops, the ATR, a well-flown target, or a CMDR bounty hunter out to make money off of your bounty.
Now add to this the instancing issue, mode switching and complete lack of ability to therefore hold another CMDR accountable, we're on to a lost cause.
There will always be instancing issues, of course. The nice thing about these changes is that they're resistant to them. The targets being attacked will be able to pose a legitimate threat to their attacker (or easily flee), the cops will be a legitimate concern for the attacker (since the cops will now be comparably powerful to player ships), and the ATR would be absolutely terrifying (since they'd be tenacious, and significantly more powerful than player ships). Instancing doesn't affect any of these mechanics, since the only CMDRs involved are the attacker and the defender, which obviously are already in the same instance.
If a player bounty hunter ends up in the right instance, it will be far more possible for them to bring the criminal to task as TTK would be far, far lower. The bounty hunter would also have the (now actually significant) assistance of the cops on their side, assuming they chose to have crime reporting on. Sure instancing issues could conceivable prevent the criminal from ever getting matched with a bounty hunter, but as I stated before, there are several other instance-independent mechanisms to keep criminals in check already.
Far better (IMHO) to rein in toxic illegal destruction using punishments of long enough duration (eg: days/weeks instead of hours), and wide enough scope (more and more station/systems denying you access). And then for the game to actually - we're approaching 4 years now - to actually offer and orchestrate some interesting PvP gameplay for those folks actually interested in it.
Not all illegal destruction is necessarily pointless, or "toxic". The majority of my illegal player kills have been for perfectly legitimate in-game reasons. The most common one that springs to mind driving uncooperative players from my hunting grounds, when I'm out bounty farming. If a player keeps stealing kills from me in a RES and refuses to join me in a wing (or I just feel like RPing a lone wolf sort, and don't want to wing), I tell them this is my hunting ground, and they need to leave. Another example that comes to mind is running across a CMDR that has wronged me or mine in the past, but is currently clean. Vengeance is one of the most classic motivators for killing. Occasional illegal player kills aren't really a problem, and are sometimes the only way to deal with unpleasant / undesirable player behavior. Occasional illegal killing isn't inherently "toxic" behavior (god I'm getting sick of that word). The problem is when CMDRs are going on killing sprees, and / or killing someone over and over. Both of these behaviors would be significantly more difficult with my proposed changes. Vastly reducing the number of "easy targets", significantly increasing the risks via increased police / ATR relevance and threat, and making it easier and more profitable for player bounty hunters to find and destroy CMDRs engaging in such behavior.
Adding massive long-lived penalties adds nothing to the gameplay, and is just a ham-fisted way of dealing with the issue. If FDev's was going to introduce crippling long-lived penalties to illegal player destruction that nobody in their right mind would choose to inflict on themselves, they may as well drop the illusion of choice and just disable illegal player-to-player damage (not a thing I want).
Are you really telling me the best ED can offer PvP wise in 2018 (after 4yrs of developement) is the notion that somehow one or more players hunting down another player not interested in combat, let alone outfitted for it, to simply blow them up (gank them) for in truth no in game reason or outcome at all, and instead simply because these individuals get a buzz out of the grief it will cause the other player, is in anyway a good position to be in? Why isn't the game more solidly penalising this and more importantly actually offering some interesting/involved (more consensual) PvP gameplay (which would of course piggy back on more interesting/involved PvE). Why enough time for CQC, Generation Ships, The Engineers v1 & v2 and Multicrew, but not for more involved meaningful PvE and PvP gameplay?
Combat is a reality of this game. Even trade ships have weapon hardpoints. Carrying any cargo at all occasionally spawns NPC pirates hunting you. Even trade missions occasionally send NPCs after you. If a CMDR has 0 interest in even the
possibility of combat, then they should head out on an exploration ships. Every other activity I can think of has some possibility of combat, either PvE or PvP (the distinction of which this proposal seeks to eliminate). The other big thing this proposal seeks to accomplish is to allow all ships to "outfit for combat" (at least in the context of a single fight) without cutting into their ability to outfit for whatever task they're looking to do. A ship specifically outfit for combat would be able to stay out in the field longer and get in more fights (things like AFMUs, repair limpets, or any other field-endurance modules FDev might release), but their single-fight performance would be on-par with a ship fit for any other activity.
Adding new meaningful PvP activities isn't really in the scope of this proposal- it's more about making the game balanced, and setting the stage for such activities to exist in a balanced, well-integrated form. That said, making player bounty hunting both more possible, and more profitable seems at least like a small addition of meaningful PvP to me. My proposal is more about fixing the foundation, than adding more stuff on top of it. Fix the foundation first, then worry about adding a prettier building on top of it.