I would definitely try what the Commander mentioned. I remember when I first started weight lifting, I had the same exact problem. I had to put on some mass on my traps which cushioned the weight in addition to what the Commander said. I'm assuming that most women wouldn't want huge traps though. If creating a shelf doesn't alleviate the problem, you still have a few other options as well.
1. Use a pad or wrap a towel around the bar to provide cushion.
2. Perform front barbell squats.
3. Perform dumbbell squats.
4. Perform dumbbell front squats.
Just a few options you can choose from and still use free weights.
Anything worth having is never easy to achieve.