I took my 2008 Cannondale Synapse Fem 1 to a local mechanic to get the shifter cables replaced and the bike came back with the shifter cables crossed underneath. Instead of the left cable running down the left side, he brought it around to the right side, then crossed it underneath, back to the left side. He did the opposite on the right side. When I asked him why, he said to prevent the rubbing you are talking about... I think you can see what he did in this picture. The crossed cables underneath bother my sense of order a little bit, but not nearly as much as the rubbing paint. And the only time I really see it is when I am cleaning my bike on the stand. It's hard to see in the picture, but the cables do not lay against the head tube anymore... there is a good 3/4" clearance.
"No hour of life is wasted that is spent in the saddle" -Winston Churchill