They don't always get penalized. I played a team in one of the last series of the season that had run out of catchers and had relief pitchers behind the plate. Being at home, I tried running on him with anybody who had decent SB numbers, but my effort backfired as the Relief pitcher pretty much turned into Jose Posada behind the plate.
Granted, he threw a couple into center field, but his Caught Stealing percentage had to be well above average.
dn