Touching up ebony wood stains  

Black markers
of various sizes are the magic remedy for such damages. However, some black finishes aren't as dark as marker ink so the "repair" will show as too dark. And of course the textural damage remains. But until the parts are stripped, filled and refinished, this intervention will "take the curse off of" the gouges.
A fine-point Sharpie will probably be the most useful tool.

Thanks, SDR...
I figured as much. Would a fabric marker do better? It's an old finish with very little sheen. With the fabric marker being more muted I was wondering if that might be the better choice.

Sharpie
I use a black Sharpie and immediately rub the ink while it's still wet and sort of smudge it in and around the scratch. This sort of lessens the difference between the sheens.

I'm glad someone else made the suggestion
of using a permanent Black Magic Marker, because I'm sure plenty of knowledgable furniture finishers would be horrified, but if it's old and you're refinishing the whole thing,I can't imagine that a bit of magic marker will hurt the piece.
I've always lusted after Bertoia benches and I don't know if I've ever seen an ebony one.
Lucky you!