I'd sooner blame the woeful engineering system than the gankers (who will always be there). The power gap between even minimally engineered and "stock" ships is so extreme that there is literally no possibility of defence or escape, let alone fighting back. Sure there were some balance issues before (SCBs were a mistake) but the performance gap between E-rated and A-rated is minuscule compared to the difference between A-rated and grade 5 engineer A-rated. The time to kill has fallen from "you might highwake if you boost past them and fly smart" to "you're dead in 0.68 seconds regardless of what you do"
I had a similar scenario flying a passenger Anaconda recently. Interdicted by an engineered imperial clipper (yes, the one with only 4 hardpoints that need gimballed weapons to be of any use) and I was dead in less than 5 seconds. I had shields and around 1000 hull. I wasn't mad at the ganker, he's just doing what he does best, likely out of boredom. I was annoyed that there was absolutely no way to defend against him while still maintaining a ship loadout that does what I wanted it to do at the time, ie run passengers.
The engineering imbalance is at the point where if you want to outfit a ship to survive random attacks by combat vessels then you have no choice but to outfit it for combat or defensive flight, if you compromise on hull reinforcements or shields for cargo or passengers or exploration you don't stand a snowball's chance in hell of surviving the opening volley.
The whole system needs to be torn apart and redone from the ground up. Make it a system of actual tradeoffs rather than flat upgrades with no penalty if you get a decent enough roll. No more randomised crap, give us sliders for each stat that are mutually bound to their counterparts so that if you increase one (like integrity) you get an equal penalty in the other (like mass) in a fixed and predictable fashion so that you can actually tune your ships module by module to get what works best for you out of them, be it mitigating a ship's weaknesses in exchange for its strengths (say, trading speed for durability or heat tolerance) or maxing out its strengths in exchange for magnifying its weaknesses. It'll all depend on the intrinsic characteristics of the ship you're tweaking and the purpose you want to use it for. No more flat upgrades turning every ship into both an unstoppable force and immovable object. That's what this system was supposed to be to begin with wasn't it?