No, I wouldn't pinch the wires under the lid either. I've always just ran my thermo wire through one of the holes in the lid vent damper. If you're careful, you can even lift the lid by tilting to the side without messing up the location of the probe inside the grill. It's not 'ideal', but I'm somewhat of a purist, and don't like drilling extra holes I can't later close up with the welder.
If that's not good enough for you, then get out the drill...