I only leave the pins in when I can't get it to stay in the right place any other way. In those instances, I slowly sew a stitch length away from the pin/pins, then hand crank the machine over it that way if it does hit a pin it's barely touching it and can be moved enough to sew past it.

A lot of times I will pin to the left of the needle so that I can pull the pins back some without totally removing them.

The only time I broke a needle was when I was free motion quilting and ran over a safety pin. I took the machine apart and did a good cleaning and oiling. Then started relying more on spray basting rather than pin basting.