The Collaborative International Dictionary of English v.0.48:

Disagree \Dis`a*gree"\ (d[i^]s`[.a]*gr[=e]"), v. i. [imp. & p.
   p. Disagreed (d[i^]s`[.a]*gr[=e]d"); p. pr. & vb. n.
   Disagreeing.] [Pref. dis- + agree: cf. F. d['e]sagr['e]er
   to displease.]
   1. To fail to accord; not to agree; to lack harmony; to
      differ; to be unlike; to be at variance.
      [1913 Webster]

            They reject the plainest sense of Scripture, because
            it seems to disagree with what they call reason.
                                                  --Atterbury.
      [1913 Webster]

   2. To differ in opinion; to hold discordant views; to be at
      controversy; to quarrel.
      [1913 Webster]

            Who shall decide, when doctors disagree? --Pope.
      [1913 Webster]

   3. To be unsuited; to have unfitness; as, medicine sometimes
      disagrees with the patient; food often disagrees with the
      stomach or the taste.
      [1913 Webster]

   Note: Usually followed by with, sometimes by to, rarely by
         from; as, I disagree to your proposal.

   Syn: To differ; vary; dissent.
        [1913 Webster]

Moby Thesaurus II by Grady Ward, 1.0:

115 Moby Thesaurus words for "disagreeing":
   alienated, antagonistic, antiestablishment, antipathetic, assorted,
   at cross-purposes, at loggerheads, at odds, at odds with,
   at variance, at variance with, at war, averse, breakaway, clashing,
   colliding, conflicting, contradictory, contrary, contrasted,
   contrasting, counter-culture, cranky, cross, cursory, departing,
   deviating, deviative, different, differentiated, differing,
   disaccordant, disagreeable, discordant, discrepant, discrete,
   discriminated, disharmonious, disinclined, disjoined, disobedient,
   disparate, disproportionate, dissentient, dissenting, dissident,
   dissimilar, dissonant, distinct, distinguished, divergent,
   diverging, divers, diverse, diversified, forced, fractious,
   grating, heterogeneous, hostile, immiscible, in disagreement,
   in opposition, inaccordant, incompatible, incongruous,
   inconsistent, inconsonant, indisposed, indocile, inharmonious,
   involuntary, irreconcilable, jangling, jarring, many, motley,
   multifarious, mutinous, negative, nonconforming, opposed, opposing,
   out of accord, out of whack, perfunctory, poles apart,
   poles asunder, recalcitrant, recusant, refractory, repugnant,
   resistant, sectarian, sectary, separate, separated, several, sulky,
   sullen, unconformable, uncongenial, unconsenting, underground,
   unequal, unharmonious, unlike, unwilling, variant, varied,
   variegated, various, varying, widely apart, worlds apart