Sorry for the late reply, just caught the thread.  This
may be the best way for your application, since putting the
header on the other side will make you know for sure what
you're using it for, at least if it's not 4 AM when you're
doing it.  But from hard experience, two things:  First, in
an emergency two cables connected with header pins will
reverse the sides, and are cheaper than redoing a board for
low volumes if something's swapped and the connector HAS to
be on the correct side of the board.  Second, if you have
the room, a third line of holes routed to the first line
with line two in the middle makes things easy.  Put the pins
into lines 1 and 2 for one way, 2 and 3 for the swapped
pinout.  A variation of this, you can even put a full second
connector worth of holes, shifted .05" over and .05" down,
but to do this you need tight holes, thin pads, and the thin
round header pins instead of the square pins helps too.
Link the inner pins pads and route the outers around.  Gets
hairy and twice as many holes vs 1.5 times for the other
way, but cuts the board space by whopping .05" x length of
connector.
  Good for prototypes and things you need to be able to
reverse the pinouts for, like different manufacturer's LCD
displays.

Don McKenzie wrote:
> As the board is also multi purpose, it's only when you want to use it as
> a pod or emulator mode, that the connector needs to be mounted on the
> solder side of the PCB.