Try these 2 ideas on some scrap engraving before you use it on the finished pen. Try some Liquid shoe polish, black or brown depending on your wood. If the wood is sealed then there shouldn't be any running of the liquid. The other idea is craft paint from Walmart, Michaels, Hobby Lobby. This is thicker than the polish but can still run in the unfinished grain of the wood. Wipe it in like putty and wait a few seconds and wipe off. We lasered 1,000's of pens and this is how we did it. Although I'm sure there is a better way out there.
PS (this message comes from (Trojan, Knight and Bulldog territory over in Cruces, by way of Wildcat country in Clovis)