You discovered the one real downfall of glass over a soft wood.
Use artists oil paint to match the wood and then varnish over once dry or tacky. (burnt sienna and a little yellow) I experimented endlessly over the years on my white ding marks and any intervention into the wood just creates a more noticeable dark mark. Or, live with it as the others suggested, but I know whats its like on a new boat.
If you have an artist friend they could do it for you. Its only a 5 min job for any experienced oil painter and they have all the colors etc.