It won't hurt it, but do yourself a favor and remove the belt so you can spin the rotors by hand from the pulley. Otherwise you'll only get a small clean spot. Let it air dry for at least an hour before starting. You'll have a pool of TB cleaner in the lower intake.
Hell, by the time you get the TB clean and back on, the intake should be dry. Do the SC first, then clean and dry the TB. Just make sure not to put the MAF back in until VERY last, so the inside of the MAF passage is dry.