Yeah, I still doubt she meant to offend; but sometimes you can say things without realizing how other people might take it. People in the public eye make so-called gaffes all the time; rarely is the offense intentional, just foot-in-mouth disease.
Even though, as you mentioned, you can't change what's in her inbox, since you said you were very interested in my points, I'll go ahead and make them:
You didn't state it explicitly, but you implied by where you put the sentence that the visit with Martin Van Buren took place between the expulsion from Nauvoo and the westward pioneer journey, i.e. about 1846-1847. That meeting (the first, at least with President Van Buren) occurred 29 November 1839 as the Prophet sought redress for the Missouri persecutions.
The circumstances surrounding the assassinations of Joseph and Hyrum were more complex than you suggested (and more complex than I intend to summarize here). The incarceration, however, stemmed from the destruction of the Nauvoo Expositor press, which, after much deliberation and determining that they were within their rights to do so, Joseph, as mayor, did order destroyed. This created a public outcry, and as a result, Joseph ordered martial law to protect the community from mob violence.
Finally, about two weeks after the destruction of the press, Joseph surrendered to authorities with the personal promise of protection from Governor Thomas Ford. He was charged with riot for destroying the press and treason for declaring martial law--defensible charges, certainly; nevertheless there was a cause which led to those charges. Joseph and his companions were incarcerated in the Carthage jail to await trial, which, of course, never happened as the assassination took place two days later, the governor having broken his pledge of protection. Had they been given a fair trial, it is likely that they would have been found "innocent of any crime, as they had often been proved before" (Doctrine and Covenants 135:7), but I feel that saying that they were "being held for crimes they hadn't committed" is a little simplistic. Rather, the acts which they had committed were accused of being crimes of which they hadn't been proven guilty.
Also, statehood was granted in 1896. The manifesto was issued in 1890.
Of course, your point in reviewing some of the persecutions in LDS history was valid, saying that Mormons love and accept others despite perhaps having cause not to. Implying that we are intolerant could equate us with, as you said, Islamic extremists, like Al-Qaeda and the Taliban. And if that were the impression being created in her readers' minds by not being clear, as Eric pointed out, about her definition of tolerance, then that would be irresponsible, like you said. But again, I think the root of the problem lies in a flawed survey, rather than a columnist's celebration of Americans' tolerance (living with others' differences)/tolerance (holding all ideas to be equally valid).