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With verbs having already a sense of division, solution, separation, or undoing, the addition of dis- was naturally intensive, ‘away, out and out, utterly, exceedingly’, as in disperīre to perish utterly, dispudēre to be utterly ashamed, distædēre to be utterly wearied or disgusted; hence it became an intensive in some other verbs, as dīlaudāre to praise exceedingly, discup&ebreve;re to desire vehemently, dissuavīrī to kiss ardently. In the same way, English has several verbs in which dis- adds intensity to words having already a sense of undoing, as in disalter, disaltern, disannul.
And the OED agrees with Etymonline that disgruntle comes from this sense of dis-, plus the frequentative of grunt. Even so, our definition isn't terribly helpful: until I read the OED's explanation, I had no idea what it meant. It needs a rewrite.