How to snip pin off .05" pitch header
Often times you can push the pin out of the connector body instead of cutting it off. This would be applicable for connectors that are not already soldered to the circuit board.

Sometimes for small pins you can twist them off using a pair of needle nosed pliers.

Do note that cutting pins off with some cutter tools that have precision ground fine point jaws can be the death of the cutter. So use care when studying the problem and avoid being tempted to cut pins with your 70$ / pair Erem cutters.