Leaving a pin in the seam line is fine - as long as the needle doesn't hit the pin.
I've also had a needle break on a pin while sewing a seam - and the broken part flew in my face.
It also roughs up the needle or can bend the needle if the needle doesn't break.
If this is an AGAIN situation - maybe sewing technique/method should be changed?
A really really drastic solution for holding some things together - is hand basting! It does work! It does take a few minutes and it does require getting out a hand sewing needle, thread, and possibly a thimble. But for some situations, it really is an effective way of temporarily holding layers together until one can machine sew it. And there is no goop or glop to clean up later, either. And hand basting can be removed much faster than a machine stitched seam that is wrong.