OK, Major Dan's post may have been satire, but their was a grain of truth in it. If you lack the flexibility to do front squats without pain, you have three choices:
Work on your flexibility until you can do them without pain;
Keep doing them even though it hurts; or
Stop doing them and find an alternative.
The question you have to ask yourself is "Why do I want to do front squats?" Obviously if you want to do Oly lifting, you have no choice. Otherwise, though, you can look for alternatives that achieve similar results but don't hurt. There's no rule that says everyone has to do front squats, or that your body development will be unbalanced if you don't do them.
As an alternative for strengthening quads, I'd suggest you try pistols. Once you get up to a reasonable number with bodyweight, start doing them with a dumbbell or kettlebell for added resistance. Then you can start doing them standing on a bench so that you can go lower.