I'm so sorry she didn't make it. It wasn't because of the surface wound you stitched. You did a great job sewing her up. I've sewn up many, many hens using regular needle and thread and no, you don't have to go remove stitches - they'll eventually just fall apart on their own.
I'm guessing the nail may have punctured an internal organ or she injured herself trying to get free or obtained internal injuries when the board fell on her or just got too stressed to recover. You did the best you could do for her.
Now if you ever have to sew up another hen you know you can do it. By the way, after I apply Neosporin to the stitched wound, I rarely fool with it after that. I find it's best to just let it begin to dry and heal instead of wetting/washing it each day. I used to have a great product "Furall" a yellow spray on antibacterial that would help wounds dry and repel flies. I can't find it anymore now that I've run out. One feed store owner told me they stopped making it. Pity cause it worked really well. I never had a sewn up hen develop any "issues" with a wound and I've had some where I had to put internal and external stitches. If anyone can still find the blue can of yellow spray on "Furall" I'd advice buying it to keep in your chicken medicine cabinet.
Monique "Ruth"