Can anyone provide a more detailed and/or logical etymology of the word denigrate?

Your concern appears to be the prefix de- which is used in English also with the meaning of “totally, completely”:

from which denigrate 1520s, "to sully or stain" (the reputation, character, etc.), from Latin denigratus, past participle of denigrare "to blacken; to defame," from de- "completely"

de-

active word-forming element in English and in many verbs inherited from French and Latin, from Latin de "down, down from, from, off; concerning" (see de), also used as a prefix in Latin, usually meaning "down, off, away, from among, down from," but also "down to the bottom, totally" hence "completely" (intensive or completive), which is its sense in many English words.

(Etymonline)

A few terms with de- prefix with the connotation stated above:

Decry, denote, demonstrative, default, devoid, deprivation, definitive, demean, demur, depravity, delusive, deportment, delude, decrepitude , desiccate, demure.