Some here have added wood blocks to the jack so it lifts the bike by the frame. That's probably the best route so you can avoid damaging the pipes, and also so you can remove the pipes if/when needed. I think someone even did a write-up on this with pictures, possibly in the "tricks and tips" section.
Having said that, I've always just put the bike on the center stand and used a floor jack with a small block of wood to jack up the front.