Just luck that prevented my stubbornness from causing real damage. In a way I'm glad I learned my lesson while I was stuck at a relatively low weight,though.
Basically a bunch of simple dynamic stretches of the hips. E.g. put one foot forward and bend over as far as you can with a straight back, trying to touch the floor, and up again, take a step so the other foot is out front, and repeat. Or stand and hold on to something and swing one leg back and forth as well as left/right on front of your torso.
To that I added "asian squat". Just practice sitting in the squat position as long as you can as much as possible throughout the day.
It took me a couple of months to get to the point where my back squat started going up with good form. In less than 6 months I went from hurting myself at 60kg to doing 5x5 at 150kg without pain (though keep in mind that at I had been stalling at 60kg for ages and done what I could to compensate with other exercises).
I'd recommend a physiotherapist and/or a personal trainer you are very sure knows squats properly. A lot of personal trainers are clueless about strength training. If it's technique, the trainer is your best bet. If your problem is actually flexibility, a physiotherapist or a personal trainer that's experienced with e.g. gymnastics or yoga might be just as good for you.