Thanks to dizwod for your suggested solution - I had difficulties implementing it though and so I'd like to offer my own solution for this trophy.
Use Evie, not Jacob if you're doing this after you've skilled up both characters, as Jacob's Gunslinger II skill will mean he'll take out an enemy with one shot. With Evie I found you can get three or four of these shoot before you get shot hits in before your enemy is too weak to draw their weapon again. Since you don't have to kill the enemy for it to count, this way you need to confront less enemies to get your 50.
As Evie, with your gun active (i.e. not knives or bombs), fast travel to the viewpoint at Buckingham Palace. Jump down just to the first surface you can jump to (i.e. not to the ground). Scan the area and you'll see to your right (south east) a little lower than you is a guard - he's one of the rifle carrying guards patrolling the top of the palace. Head down to him. The guard won't attack unless you do something, so kidnap him and then release him. He'll stagger a bit and then pull his gun on you. Retreat and then head back towards him until you're close enough that you pull whatever knife weapon you have equipped. Wait for the triangle 'counter shot' option to appear in front of you and then press triangle. Evie will shoot first and you'll see your bullet total doesn't decrease. Wait at this same distance and the guard will draw again - wait for the counter shot option again and then press triangle for another shoot first. Repeat this with this same guard until he is close to death when he won't try to shoot you anymore. I think most times I got four shots in.
Leave this guard and head forward and then to the left on this same level to the next rifle guard and repeat this process. There may be a third guard available if you keep heading around the square.
Once you've done all the available rifle patrol guards, fast travel to the viewpoint at Victoria Station and then fast travel back to the viewpoint at Buckingham Palace, where all the guards should be reset back to full health and starting position. Repeat these steps until you get the trophy.
I recommend this approach, using these rifle guards, because they don't melee you unless you get right on top of them or too close when they're almost dead. On the ground, the guards would just chase me and try to melee me and it was difficult to get them at just the right distance for the right kind of shoot back opportunity to present itself.
Also I noticed that not all of these counted as proper counter shots (in perks) but they obviously counted for the trophy. When my trophy popped, I had 12 of 25 counter shots registered - it seemed like only every three or four attempts did it count as a counter shot for perks.