I just finished revising my paper "Moral Conviction and Disagreement: Getting Beyond Negative Toleration." There, I suggest that tolerance construed as merely "putting up with" is not a sufficient ideal for cultivating a genuine community. I also point out that seeking to engage tolerantly with those with whom one has strong moral disagreements is not a threat to one's integrity. (This might seem to be a threat, insofar as one might feel that the request to be tolerant asks one to put up with things that one finds intolerable.)
As always, this is only part of the story. In my recent Philosophy Now essay, "In Defense of Intolerance," I focus on something I discuss briefly at the end of the revised paper above, which is that sometimes intolerance is the right attitude. Sometimes one will find it impossible to tolerantly engage with those with whom one disagrees. What then? There, I focus on pointing out that "what then?" is an entirely separate issue from whether one can or cannot tolerate something (or someone).
A great deal of my interest in this topic was driven forward by reflecting on Scott Roeder's murder of George Tiller. I'm still not quite happy with something I say in the Philosophy Now essay, which is that I am not happy allowing that violent intolerance is ever justifiable in the face of moral disagreement. I say, "I must ask what right I have to...risk someone else's life on the chance that I'm not mistaken - especially when that person has not consented to the risk." The obvious instantiation of this point is that I have no right to go around killing members of the so-called Tea Party. But this gets to the difficulty with my comment in Roeder's case. I'm not so much worried about the actual case, because Roeder shot Tiller dead in the lobby of a church. Utterly awful. But someone might spit my words back at me and ask, "What right does Tiller have to 'risk the life' of the fetus [viz. abort it] on the strength of his convictions?" I think, however, that the right answer here is that one could only ask that question by failing to pay attention to the details of the situations in which Tiller was involved. This isn't to say that such attention to details would lead one to accept or endorse Tiller's choices. But would I really be begging any obviously answerable questions if I said that any sane, judicious person would realize that the abortions Tiller performed were surrounded by complicated, unfortunate, and often tragic circumstances? (See here.) The difference between Tiller's decision to save and help those women (and girls) and Roeder's self-described choice to save unborn babies from Tiller is that Roeder acted from an abstract principle and Tiller acted in response to complex, concrete, and often tragic circumstances. Thus, Roeder's act shows what can happen when we put principles above individuals. We can convince ourselves that our principles make the murder of others ok. But maybe I'm making a mountain out of a molehill, since Roeder, a Christian in name, simply failed to love even his enemies.