I clean all the mechanical parts, but I don't use any sort of brush to scrub the barrels. I have some camo parachute cord type stuff that Walmart sells in the camping section that I tied a bunch of knots in, and a string with a weight on it so I can pull it through the barrel. I squirt some Super Lube in the barrel before I pull the rope through. A couple dozen knots and 2 or 3 passes and the barrel is nearly spotless, and left unscratched.
My Ruger MKII used to get so dirty in only a few hundred rounds that it would start jamming. I decided to try something different for lube since none of the oils and greases I'd previously tried worked that well. I took the bolt out and hung it up and sprayed it with a heavy coating of Super Lube, then left it for several days so the solvents would evaporate. I then used a cotton cleaning patch to rub the oil and teflon into the surface as best I could. I sprayed it down again and hung it up for several days to build up another layer of the oil on it. It's slick as snot, and the bolt slides freer than it ever has. I've since fired about 500 rounds through the gun, and the inside of the action doesn't look any dirtier than it did after only 50 rounds using Break Free CLP, Tetra Grease, and any of the other lubes I had tried.