Knee pops during pistol squats

I'm pretty much a beginner, i started working out legs only recently, before that i would only do leg extensions every once in a while.
I was doing pistol squats on my right leg, I could go decently low... Then my knee popped. At first it only felt funny, i stopped the workout and went to bed. This morning i tried to bodyweight squat just to check and yes it hurts a little when i try to go low...

I'm probably going to have the doc check it, but the idea that a knee could be injured with such a small effort ( what would happen if i dared to try a real squat?? ) is frustrating.
Do you think i can still do leg extensions? I guess i can do leg curls, glute ham raises and hypers for the rest of the leg (Maybe also hip thrusts with a barbell?) But what are my quads going to do 

Oh well i guess it's better than, say, an  injured shoulder or lower back  Btw yes i do have a history of weak joints (well, weak everything i guess)

What do you think? Can i keep working out legs with auxiliary exercises?

The knee is probably one of the WORST places to get injured.  My knee is the reason I can no longer squat.  Do what your doctor says.  One of the dumbest things a human can do is say "well it doesn't hurt that bad" and continue working out.  Because YEAH it may not hurt that much now because it's probably nothing horribly major (might be a bit rough but you can probably get it healed up) but if you keep working it I can promise you that you will not only end your lifting career (for lower body) but also it will make your life a hell of a lot worse.  You don't just use your knee when you work out!  You use it when you walk, run, go up/down stairs...pretty much everything that involves movement.  6 weeks out of the game is a whole lot better then 60 years.  Stay safe man!  

I don't even have a routine yet. I was just trying out various exercises to decide which to include and what weight i needed.
I tried: pistol squats, leg extensions, split squats, glute ham raises.

Maybe it's the fault of the glute ham raise? (I had to try it while bending over at 90 degrees, it's way too difficult to do it with your body straight) the back of my knees are strained a lot during that exercise.

It may be relevant that i do a variation of the leg extensions - i did bodyweight leg extensions, that is i sit on a bench, tie up my feet at the end of it, and put something robust below my knees. By extending my legs i lift up my upper body. It's like a regular leg extension, but your feet are kept stationary and it's your upper body that goes up instead.  Very similair to this: http://www.exrx.net/WeightExercises/Quadriceps/WTSissySquatAp.html
Do you think it matters?

Anyway yeah i'll just stop until i have the doc's verdict.

While i try to find my camcorder to record form, How do you screw up a pistol squat? By going too low?