When a ship is a hunter-killer, send a faster ship after it, fight it for a while, then once it gets low, most HK's will start trying to get away(you can tell by a "Them Scurvy dogs trying to get away") in the bottom of the intercept screen where hits appear.
Let them run away out of the intercept window, that makes them stop being a Hunter-killer and engage them again, after that they'll crash normally.
By the way, other people have found that you don't even have to leave the interception window, but to be certain, I recommend that you do.