This “in the name of” construction appears frequently in anti-Cordoba statements: It’s a conventional usage that anyone might employ non-controversially, but acknowledging the obvious – a connection or association between Islam and 9/11, even the implication of some traditional Islamic teachings – is different from establishing the responsibility and accountability of (all) Muslims.
Religion is not a skin color, and I think it's high time that Americans started to realize it. If a person over eighteen is voluntarily pledging faith to a religious text that calls for the extermination of Jews, the subjugation of women, and the conquest and destruction of the rest of the world -- it is not unfair to "discriminate" between him and another citizen.
Religion, at least for adults in a free country, is a choice. Anyone who calls the Koran a holy book after 9/11 is willfully associating themselves with that atrocity, and we have no obligation to blind ourselves to it.