From the pic you showed and your comments, you wanted a "clean" look on the worm holes and as you have experience, CA will tend to darken the wood and it would happen with almost all other products.
The one way I know it works is to cleaning the inner surface of the worm hole with a Dremel tool and one of those small dentists bur bits and very carefully remove the dirty surface from inside the holes, after that use some Liquid Gloss or Liquid Glass as is commonly known and fill those holes using a needle or something very pointed to prevent any air bubbles to stay trapped, this product is extremely thick and self-levelling so, you may need to do one part od the pen/barrels at one time and after set, rotate and continued on.
I should also remind you and everyone else that, unless this piece of wood/pen is of great significance, the time it will require and the cost of the liquid gloss, most will be wasted, will be something that you need to be aware before you embark on such task.
Cheers
George