The black pen doesn't seem to work too well imo.
I'm not sure if it would be worth getting re-anodized or not, after all its not like a Cobra or Agent where the barrel has to be, but shouldn't be removed.
This is a situation where the Cerecoat or epoxy finishes might be of some use.
Depending on how bad off the frame is stripping it might be an option, being careful not to obliterate the serial number.
I have a new, well its been shot some, but a new XSE LWT Government and somehow there is one spot where the aluminum shows through, just a little spec or dot and nothing seems to work other then ignoring it.