I'm thinking of it from an immersiveness (is that a word ?) standpoint. When something patently absurd happens, it immediately destroys the "immersiveness".
I become acutely aware that I'm just another sad, pasty sod sitting in a dark room in front of a display.
That said, I completely understand the prevailing viewpoint and will not presume to second-guess the game designers.
If the game designers would go about this immersively and with a sense of credibility, blowing up ships for failing to dock correctly would never happen.
It is a pure gameplay mechanic that has no basis in any realistic theory whatsoever.
If the docking cylinder interior wasn't indestructible due to limitations of the game engine, blowing up a ship inside this insanely fragile and vulnerable area would be the worst you could do. The explosion would send shrapnel and chunks of the ships hull everywhere... live ammunition still stored in the ship's weapons would float around freely... radioactive residue from the engine would pollute the carefully regulated atmosphere... pad control towers would be shattered to ruins, dock workers smashed to a pulp or sliced into pieces... on luxurious stations the greenhouse domes would be crashed into, endangering all people currently frequenting the park underneath... and all pieces of leftovers from the exploded ship that somehow luckily kept floating in the gravitational neutral zone near the middle of the cylinder would be crashed into by incoming ships and sent hurling off into all directions, obliterating structures on the ground level, killing personnel, destroying machinery...
Millions of credits of damage, catastrophic loss of life... And until the cylinder is cleared of debris, the risk of allowing ships to dock or undock would be enormous, so the station would have to shut down until cleared.
The Babylon 5 Episode "By any means necessary" features exactly such a problem. After a fatal accident inside the docking bay traffic on the station comes to a halt and dock workers go on strike because they have been forced to work double shifts despite some of their fellow members having died and many others injured in the accident.
For me, there is no bigger immersion-killer in the game than the "station killing ships inside docking area" bug. Yes, I call it a bug. That's not a feature. It is beyond absurd.
If manual docking is the norm, and being incompetent at it endangers traffic in the docking area, then the appropriate response of the station personnel would be to dispatch a security ship that hijacks yours or latches onto yours with docking clamps or something and overrides your ship controls, then lands you on your designated pad, resulting in a hefty fine that also pays for the necessity of having to assist you with docking. Or perhaps some weapon that disrupts all power on your ship is used to shoot you helpless before that security ship, or drone, does its job. Same if you try to shoot anybody inside the docking cylinder. Your ship systems are overloaded by an ion cannon type of weapon, you are forced to watch how your ship is docked remotely by other ships moving it down onto the pad, and you get fined or have to pay off a bounty.
This would not only be much more believable, but also more effective against griefers.