Dispute in the Orthodox Jewish is something that has always been a source of discomfort for those involved and for those reflecting back into history. Here is a couple of sources that I feel shed some positive light on the mechanism of dispute as being of a positive religious value.
"When an individual does not intend to scoff – rather only to state his belief – even if these positions stand against your belief and system, don’t say to him: “Don’t talk, seal your mouth!” For then the system will not be clarified. On the contrary, in such matters we should say: “Speak as much as you want, all that you want to say, so that you will not be able to say that were you granted permission to expand you would have spoken further [and convinced me with your beliefs].” If, however, you do close his [the questioner’s] mouth and prevent him from speaking, that points toward a weakness in the system. This [approach] is the converse of the general impression, which is that it is not permitted to discuss the system, and that thus the system is strengthened. On the contrary! That approach undermines the system! … Thus [through the former approach] a person comes to the inner truth of matters… For [after all], any hero that comes to compete with another to demonstrate his might wants very much that his opponent muster as much strength as possible – then, if the hero overcomes his opponent, he proves that he is the mightier hero. What might, however, does the hero display if his opponent is not permitted to stand strong and wage war against him?" - Maharal, Be’er Ha’Golah, end of Be’er 7 (free translation) "You should not allow yourself to be disturbed by the various disputes between the Tzaddikim(as for example the differences of opinion between the Sages of the Mishnah, the Talmud and so on). If a person is troubled by these disputes and states raising all kinds of questions about them, it is a sign that he has allowed some impurity into his mind. It is this internal impurity that is the real source of his doubts. The danger is that his doubts could grow to the point where he becomes permanently separated from the Tzaddikim and their followers, who are the source of true and enduring life. A person should understand that if he finds himself troubled by doubts and questions about the Tzaddikim it is an indication that a flaw exists within himself. If he realizes this, it will help him return to the truth (5:4)."
(Par 1, Chapter on CONTROVERSY AND STRIFE, Likutey Eitzot by Reb Nachman of Breslov http://www.breslov.org/torah/pdf/Advice.PDF )
(1) For an interesting article on the matter of Reb Nachman of Breslov’s view on the matter see the article by Rav Itamar Eldar (http://www.vbm-torah.org/archive/rnachman/21rnachman.rtf)