I use very long (and thin) pins so I can insert them so the tip of the pin falls short of where the needle will hit. That said, sometimes I insert one a bit too far and it's far enough that the needle may glance off of it. I've never broken a pin or needle from hitting a pin.
On the Sally Collins video she sews over pins all the time and said that machine speed is the difference between sewing "over" pins and breaking/bending them. I noticed she uses the same long thin pins I use.
So possibly just slowing the machine down is the answer, coupled with very thin pins.
I typically run my machine at a fairly slow speed unless I'm FMQ'ing. I think that is a product from my 7th grade Home Ed teacher yelling "quit racing those machines!!".