I'm not super sure of what to tell you in terms of your physical condition/limitations and I have no idea how much that does or does not result in your pain, but I'll tell you what I do know about getting those heels down without killing yourself.
Do lots of stretching. The best is to put the ball of your foot up on a step or a ledge and gently lean your weight into it to allow your heel to sink down until you feel a good stretch in the back of your leg... but NO PAIN. Don't stretch so much that it hurts, just a good healthy pull for about 30 seconds at a time. Here's a link about stretching: http://www.sportsinjuryclinic.net/cy...alfstretch.php
The technique I described is in image three.
When you're on the horse, imagine doing the same stretch. Getting your heels down should NOT involve using your muscles to literally pin them down in place. That typically causes a great deal of tension, muscle fatigue, and discomfort. All around, not a good thing for you to do. So, think of it as the same stretch, allowing your weight to sink down through your thigh and your knee.
Finally, don't be afraid to play around with your stirrup adjustments a bit. Lengthening them even by one or two holes can make a world of difference and sometimes we misjudge the proper length for our personal proportions/build. Yeah, there's all the "tricks" for getting close like having the stirrups line up with your ankle bones or the leathers be as long as your arm, but that's just for getting in the general ball park. It differs from person to person, so try playing with your stirrup length... and I mean literally ride with them at different lengths each time. Don't let them out, put your feet in and immediately think to yourself that it feels too weird to ride like that. Just because you're used to your stirrups feeling one way doesn't mean that that's the way they're supposed to feel. ^_^
Don't let your instructor convince you that your stirrups need to be shorter than is comfortable, either. Several jump instructors are very opinionated about how long is too long, but if their idea of a good length has you tied up in knots, you won't be riding very effectively and won't be able to progress well. You're the only one who knows how it feels and what feels best, so don't let them boss you into bucking up and toughing it out. As you progress with your riding, your flexibility may also increase and you may be able to get away with shortening the leathers up again bit by bit.
The GRAND rule of thumb: if it hurts, don't ignore the pain. Your body is trying to tell you that something isn't working out so hot, so fix it!
All of this is from personal experience, I hope some of it helps.