I believe that the "not in guild" should take care of that.
When you upload your rooster, you get a list with all characters not in the guild.
Mark those you wanna keep as not in guild and it should do the trick.
Can somebody plz confirm me on this one - since I don't use it myself?
/Misen
If you go to one of the characters in the character update screen you do have the option "Not In Guild (Hides from the Roster, but include them on the DKP lists)."
Which is not what you are looking for. You should select the "Retired/Quit" option to remove them from the DKP listing and still show them on the roster.