Bummer.  I've done this.

My fix was to round up a nail-set with a fairly small head:

Then, with great care, I'd fit the nail set's head onto the protruding nail's point and tap it up out of the deck.

It's hard to make the repair absolutely invisible.  A simple patch is a decorative "sheer stripe" like the one on this kayak:

   You might grind down the tip of the screw with a Dremel tool and then carefully cut away the damaged wood. Take something like a half inch drill and an exacto knife to cut a clean circle and then fill it with a thin piece of dowel. It will be much darker, but it will look better. Or, if you have some veneer that has closely matching grain, fit that in.

i,m with john on this...back it out a bit and then you can carefully use a claw hammer with some wood to protect the wood to pull it out the rest of the way.

if you do it carefully, you will barely notice the split as the wood will, to a large part come back together.

h

Depending on the damage to the wood, you might placing a wet washcloth over the boo boo and ironing it.  The idea is that it may cause the fibers to swell up to "heal" the wood.  Then you can sand it back down to where it should be.  I've used this trick and it often renders the blemish invisible to everyone but you.  Good luck!

   Thanks for all the ideas! John's worked great and was easy. I tried ironing which seems to have helped some. I think with a bit of sanding it will only be detectable when looking for it,  if at all. 

Been there done that. A coat of Brightside will hide a lot of mistakes!