Way back in the early 70's when I got my first sewing machine, a Kenmore, we were all sewing double knits. I was told we could sew right over the pins and I did with no problem. The knits were just stretchy enough so that the pins just kinda moved out of the way of the needle. I had straight and zig-zag stitiches. These machines were mechanical in nature and a lot tougher than modern machines.
I was told with today's electronic machines and their many decorative stitches it requires precision timing of the machine so definitely do NOT sew over pins. When a needle hits a pin it can through off the timing, which can cost a pretty penny to fix. Not to mention the safety hazards of broken needles flying about. Besides, most of us use woven (cotton) fabrics for quilting, and they do not give the way those old double knits did. Sometimes when I have seam matches pinned together, with all the seam allowances, that's several layers of fabric. Those pins are not going anywhere unless I remove them, so I do.