Has there ever been an antonym for "benefit" that includes the latin affix "neg-"?

Solution 1:

No, bene- and neg- are not used to form antonyms in either English or Latin. Their root meanings of "good" and "deny" are roughly opposed, but not antonyms in English either.

As others have mentioned, mal-, meaning "bad" is the typical antonym to bene-, as in benediction/malediction (literally "good speech", "bad speech").

Posi- may seem like it should oppose negi- because of the positive/negative pairing, but it actually comes from a root word meaning "put" or "place." Affirm- is probably a better opposite to neg- as in affirmative/negative and affirmation/negation.

Solution 2:

The Oxford Dictionaries online finds

malefit A misfortune, a disadvantage.

from their British & World English Dictionary, supposedly from the 18th century. No provenance or examples.

The printed OED doesn't record this word, but does have malefice meaning either sorcery (first attribution to Chaucer in 1324) marked as archaic or an evil deed or mischief (first attribution to Spenser's poem "Mother Hubberd's Tale" in 1591) marked as obsolete or archaic:

He crammed them with crumbs of Benefices, And did fill their mouths with meeds of malefices

(There's also an obsolete astrological use meaning the obvious thing.)

The OED finds both benefit and benefice from the 1300s. The former prospered into five major senses (including such as the kind of benefit that's a charity event); the latter fell into obsolescence, taking its antonym with it, perhaps because of its special meaning associated with sorcery. Note that malefit would seem to have arrived long after benefit.