Note that being comfortable with differing opinions and being comfortable with certain forms of creative debate are two different things. A debate should be a voluntary contest between parties and is only possible if they both share and agree upon a base set of principles as the foundation for the debate. If an atheist and a theist "debate" the existence of God(s) it isn't a resolvable argument since their divergence of principles is at a fundamental level and the only thing they share are certain derived points that accidentally coincide. In this case the parties must either be comfortable with the fact that they differ in opinions or they are not. This does beg the question as to when one should be comfortable with a differing opinion. I suspect that those who have encountered real conflict having a larger comfort area for differences due to their understanding that conflict invites real costs.
In the case where legitimate debate can occur, the rules I usually try and follow/enforce are:
1. Establish the goal all parties wish to achieve (i.e., define success).
2. Establish the point at where our agreement on methods diverged.
3. All ideas should be orphans in that they have no privileges purely due to parentage.
4. Never ascribe to malice that which can adequately be explained by incompetence or ignorance.
5. Be ruthlessly honest about your own position, to include disclosing the weaknesses you know or suspect as well as disclosing the strengths of the opposing position (especially if the parties holding that position do not know it or present it themselves).
Personally I become uncomfortable when there is unanimous agreement on positions I know to be legitimately debatable, even if I hold that position. In those instances I will promptly switch sides and argue against my own position to insure it has been properly vetted.
In my experience the point that most reliably invites emotional response is failure of #3 since it's hard to move from "my idea" to "the idea." The most insidious failure is at #1 due to either misunderstanding or dishonesty since it corrupts the entire effort but can be very difficult to discover.