I saw on the arduino shop that there's now an arduino DUE sale without headers. I was wishing it for a while..
But I wonder if there's another distributor for north america. Shipping cost from arduino shop is a too much.
I've took a look at digikey, mouser, amazon, adafruit and sparkfun.. found only the original version..
Get the board with headers, clip them off with a diagonal nipper, then use a solder sucker to open up the holes.
A lot of trouble for something that can came straight foward..
A 10-minute job to remove them.
Pull/pry the black plastic pin-header casing off, and you are left with just the pins (forks).
Put the board in a vice, so you have both hands free.
Solder/pull the pins off one by one (don't use any force).
When all done, use a solder sucker to open the holes.
A temp controlled iron is a must.