Hi, welcome to the forum!
At present CR degredation stops endless kiting, but it can still last for a few minutes, and I agree with you that it can be boring. At present the answer is: have some fast ships of your own or a carrier with interceptors. A Condor with 2 Talons is a pretty cheap way of taking out small frigates, and one can be salvaged during the tutorial. With your own fast ships/interceptors denying the enemy their 50 speed bonus, your destroyers should be able to catch up. Another possible solution is to mount a good number of Harpoon missiles with ECCM (and possibly the missile skill): when the enemy tries to poke you and takes a bit of flux damage itself, launch off a bunch of harpoons - with luck you will overwhelm their PD and pop them. On the Apogee, Locusts can do the same thing, though large missile slots are rare.
It would be nice if in future if there were a bit more logic in making the AI retreat when its down to the kiting, can't win stage, just to save the player time and avoid exactly what you are saying.