I agree w/Sean, if you scuff them & use good paint (I like VHT, better than bar-b-q paint, but >$) they will look fine & hold up adequately. Surface prep is everything, be sure to use metal prep before painting & don't handle them before you spray them after you cleaned & metal-prepped them. In time (years later), you will get stuff coming thru the paint if they are really rusty, but then you just do it again.
The best results for surface prep I have had was using a friend's glass-bead blasting cabinet. You can come close by just using a wire brush in a die grinder & then using a soda-blasting media/equipment. Harbor Freight Tools has one they run on special frequently, I got mine for <$10.
http://www.vmaxforum.net/showthread.php?t=21096&highlight=soda
The soda gets into the tiny pits the wire brush cannot, but the wire brush will cut heavy rust more-quickly than the soda media will.
Aesthetically, I just don't care much for the wrapped-header look. Around Miami, about every other H-D Sportster going for the 'bobber-look' has that done. Now maybe if you
painted the wrap after you wrapped it, then you would be a
Trend-Setter! Go for a contrast. That beige look it goes-to after a few heat/cool cycles just looks what our British friends would call, "tatty."
Painted wrap would at-least make yours
look different.
The stock front main pipes are double walled so you can either scuff and paint with high temp paint or wrap them - either way will work fine. The rear is the hottest set of pipes though they will still normally let a good high temp (BBQ or exhaust header paint) will hold up.
Sean