It should, why not?
Well for discussions sake lets pretend each airline or civil aircraft manufacturer invests billions of dollars to develop technologies military forces spend to defend their aircraft... even if they make a major breakthrough and develop something that works surely if any airline around the world needs to get access to use them then it would be very easy for Chinese airlines and Iranian airlines and North Korean airlines and Cuban airlines and other airlines from around the world to buy these systems and fit them on their aircraft... but their national militaries might be interested to have a look too... and copy and use on their own military aircraft... once the systems are widely deployed and missiles stop shooting down aircraft in numbers except drones which wont be cheap any more if you load them up with anti missile systems of course, then the makers of missiles will need to look at those new defence systems and work out HOW TO DEFEAT THEM.
They will then upgrade all their missiles to defeat those defences so those billions spend developing the systems and the billions more spent putting them in to service just got wasted and they need to upgrade them again... more billions to upgrade more billions to install... we are talking more than the cost of the F-35 programme... trillions... but no known anti missile countermeasures can defeat SOSNA and Pantsir in optical mode and the TOR system is pretty impressive... I don't think they would be defeating that very easily either...
The best things you can do is enforce some important rules like no turning lights off in flight... and no flights without using civilian flight codes... and serious responses to countries like the US that turn off their transponders in military aircraft and sneak around doing things they shouldn't be doing, or like when US aircraft pretend to be civil aircraft when they are not.
With regard to your list I would add that Russian plane that the Ukrainians shot down on its way to Israel, and also the military but also used by civilian Il-20 Russian plane shot down by Syria.
The solution in the latter incident which was engineered by Israel to use a Russian plane as a cover for its attacks was to give the Syrian air defence force a much better view of their airspace shared by all its air defence forces... it makes accidents much less likely... but accidents will always happen.
When the USS Vincennes shot down an Iranian A300 Airbus in the late 1980s there were a lot of contributing factors and a lot of things that went wrong that could have prevented what happened... very simply Iranian speed boats (the Americans called them boghammers, but they were actually Iranian navy patrol boats) were reported as being active and a recently arrived state of the art AEGIS class cruiser... the USS Vincennes roared over into the fray to swing its new untested dick around to impress everyone about how big it is... they launched their helicopter to arrive first and see what was happening and the Iranian boats fired some warning shots to basically tell it to fuck off. The captain of the Vincennes decided that his helicopter was "under fire" and therefore he was free to use any force he thought necessary without getting permission... he had been talking with the area commander asking permission to go in and clean up those speed boats but was getting refused. There was a carrier in the area but after hearing the radio traffic from the commander of the cruiser he pulled his aircraft back because he feared this idiot might shoot them down in error... he wasn't far wrong... but having those Tomcats in the air could have solved so many problems... they could have approached the target and circled around from behind and seen it was clearly a civilian aircraft transmitting the correct civilian code on a civilian flight path... running a bit late but in the right corridor and it was also climbing rather than descending as the crew on the Vincennes claimed even though the recorded details of the incident showed it climbing to normal operational altitude with no suspicious manouvering...
The primary problem was a software and hardware design fault... a human computer interaction (HCI) fuckup.
The airbase the airbus took off from was a joint military and civilian base and as the Airbus was getting ready to take off it sqwalked its civilian ID code... the operator on the Vincennes used his mouse to move the cursor over the aircraft to check its details. The system followed the aircraft taking off with the information box following the aircraft in flight but it didn't move the cursor that highlighted the target so the cursor was still on the airfield where other aircraft were preparing to take off too including an F-14... so you start out IDing it as a civilian aircraft but after it takes off it stops sqwalking the civilian code and emits a military code because there is an F-14 sitting on the airfield waiting to take off that has powered up and is emitting its military code... so the operator sees the system tracking the airliner but is getting the information from the cursor which remains over the airfield even though on his screen it appears to be following the civil airliner... they try to contact they plane but even if they could receive military frequency messages they would ignore it because they are not an F-14 to which the messages are being directed... the F-14 on the airfield wont respond either because he is not in an F-14 approaching a US ship inside Iranian territorial waters where they chased these Iranian patrol boats too... firing 127mm shells at speed boats because those speed boats fired some warning shots with a heavy machine gun.
We all know what happens next... no response and a belief the Airbus is an F-14 and is descending flying towards the ship they try to launch a Standard missile... there is a fault and it takes 90 seconds before they launch SAMs and shoot down the aircraft...
How do we know? There was a film crew on board filming a doco and of course we got the results of the investigations too.
The point is that once that missile is launched there is often not much any aircraft can do...
It is easier to steer civilian aircraft away from testing areas, war zones, and places of high tension...
If Indians are to be believed, they shot down an F 16 last year, despite the fact that F 16s have onboard jamming system. But that could also be due to pilot error.
Even if you don't believe them Israeli F-16s have been shot down too... in fact most combat types have including a Backfire to what was probably a BUK in Georgia...