When Dwarf Therapist picks up an illegitimate dwarf (mine shows a hostile captive were-beast and one dwarf who was kidnapped years ago) you could change their profession and nickname to something identifiable and unique.
Examples: ["nickname" name, PROFESSION]
- "VampireFace" McLastName, VAMPIRE
- "Wereskink" McLastName, ENEMY
- "zzSo-and-So" McLastName, DESCRIPTION
And so forth. It won't get rid of them, obviously, but it makes it easy to disregard their labor assignments when listing by profession and/or name. The last example would work exclusively to put them at the bottom of an alphabetical list, if you find yourself sorting that way most often. I put my custom profession names in all-caps to easily tell which ones I've made, but that isn't exactly necessary. =)