Rubbing alcohol (isopropanol or 2-propanol) and denatured alcohol (ethanol) are two different chemicals entirely. Rubbing alcohol is VERY safe to clean a pipe with, and even safe to make solvent-extracted hash with.

If you are going to use a mechanic's cleaner on the pipe, I recommend following it with an isopropanol wash and then hot water rinse as Woooo described to remove any remaining solvent.

As for a final step to get rid of the smell... try soaking it in Listerine for an hour or so. Minty-fresh!