I am not a physical therapist,and I don't know any specific exercises to strengthen that area.I think that the general leg exercises (squats,lunges etc.)should help.In squats,make sure you don't bend your knees past 90 degrees.
The way I look at it,swimming BR kick is a very unnatural movement that places extreme strain on the knee joint,much like pitching a baseball does on the shoulder.I warm my knees up very slowly for each swim,going very,very slow BR to slow BR to moderate BR for at least 250 yds before I do any race pace work. Then I have the equivalent of a "pitch count"for swimming BR.I never do more than 85 BR kicks at race pace in a workout.85 kicks is my goal stroke count for 200M so that seemed like a necessary limit.I do the rest of my race pace BR as BR pull with dolphin kick(with or without fins) and leg work as eggbeater kick.I find eggbeater puts less strain on my knees.If my knees are feeling especially twitchy I will narrow my eggbeater until it is basically a bicycle kick. If my knee is a little twitchy I ice it after the workout.If it is sore,I wait until it isn't before I swim BR(at least I should,if I have a taper meet coming I'll skip BR for a couple of days,but then I get paranoid about losing my timing and "damn the torpedoes,full speed ahead"figuring I can rest after the meet.This is probably a very stupid thing to do.)