The curtain airbag squibs run down the entire length of the truck, front to back. The wire connections are in the back. I didn't see any special instructions about the pillar garnish removal procedure so I think it's probably safe enough to remove. To be extra cautious, you should disconnect the battery and then wait 5 minutes before working near the bags. After you remove the garnish you'll just have to see if you can get at the wire bundle or not. If not, you'll need to drop your wire all the way down to the underdash area. In either case, just make sure any wires you run don't interfere with the deployment path of the bags -- wires should run above or behind the squib and be appropriately fastened so they don't move.
Good luck!