I'm curious why you would run or reach when the squall hits. I would think you would want to beat into it so as to get past the heavy stuff on the leading edge quickly. You also present less area to the wind that way. Less tipping force.
If you're beating into it, have the sails sheeted in hard, and you get a squirrelly puff of strong wind across the beam, you can take a knock-down. You might get headed up in a puff while reaching, but a knock-down is unlikely.
Also, you're moving perpendicular to the axis of movement of the squall when reaching, so you're going to get out of it pretty quickly.
Have one of your crew keep a sharp watch for other boats and obstructions--the rain in some squalls is so dense you can hardly see the bow of the boat.