In my opinion the best way to deal with it would be to stop making PvP-PvE contact so one sided. If you want to mine then you want to mine as efficiently as possible. In Open though, you need to compromise to account for hostile CMDRs. But compromises affect efficiency, and you're also not going to beat someone at PvP in a hybrid ship, you're only really looking to escape, not dish damage back. So then someone being practical about it looks at it like this "I can either do my stuff efficiently, without worry about other players, and play in PG/solo, or i make a compromise in my loadout, for less efficiency, play in open, with a chance that i'll get attacked, and if attacked, i might escape or i might lose hours of effort to someone who is risking nothing".
That last part is one of the most interesting as well. The attacker really risks nothing. If they really mess up, they might lose their ship (for example, they are so focused on their target they don't notice another player coming up behind them).
One sided PvP, both in terms of balance and risk, for most people is not interesting. Who is interested in this sort of PvP? Griefers, gankers, and people who suck at PvP against decent opponents but want to kill people to stroke their egos.
Therefore, in my opinion, the only way to address this is to do balancing which results in the ability of ships to be just as dangerous when doing PvP as they are when doing PvP without impacting their efficiency doing those activities. That would add balance to the situation and provide risk to the attacker.
Unfortunately, i don't think this is possible to do in ED, at least not without making such changes it probably wouldn't please anyone.
Its quite similar in GTA. You get a mission to deliver stuff in a postal van (for example), which is of course unarmed and slow... it literally crawls going up hills. The game alerts everyone in the lobby you are doing this. Death means you lose it all. All around the lobby are usually people flying broomsticks (Opressor Mk2, a flying bike, fast, agile, has countermeasures, fires homing missiles) just looking for people to kill. In most public lobbies you won't stand a chance of making a delivery unless all the "PvPers" are busy. But if one takes notice, you're dead. You're on a time limit, you can't mess around, those post-op vans are slow. Getting out of your van to fight back leaves it vulnerable to attack, if the van is destroyed, mission over.
Of course, you know what the attackers say? Things like Git Gud and The game allows it and don't play in public lobbies then! (those missions can only be done in public lobbies, its like the idea that open only proponents like to push).
What do a lot of people do, included those self-styled PvPers? They force solo public lobbies, through firewall hijinks, "testing NAT type", or suspending process, all of which push you into a solo public lobby as the game thinks you are lagging out and doesn't want you to affect other players (by the way, GTA also uses P2P networking). Another method people use is make groups where they ensure the whole lobby is filled with friendlies, others who are grinding, so griefers/gankers are less likely to get in.
So, anyone who seriously wants money, and not the risk or challenge, simply ensures they don't get matched with those looking for PvP. Result, public lobbies are generally full of people flying around on broomsticks killing each other. Its just crazy. I logged in yesterday and before i finished loading i got a message that my personal vehicle had been destroyed. That's how crazy it is as time.
In short, you can't have a mix of PvE and PvP play going on and being fun for all unless everyone is on equal terms with equal risk for all (of course, skill should still be a factor, the only real significant factor).