Here are some some other quotes from the article, in order of appearance, to start with the tolerance part:
"Compulsion is contrary to the meaning and purpose of religion" "Islam does not allow . . . non-Muslims to be forced into accepting Islam""As we know, faith is a matter of the heart and conscience, both of which are beyond force."
Although the next paragraph appears to be a little more grim, as it divides people into just two groups, believers (to be read as muslims), and nonbelievers (anybody else).
"However, the powers of unbelief always seek to coerce believers away from their religion and their faith. No believer has tried to coerce an unbeliever to become a Muslim, whereas unbelievers continually try to lead believers back to unbelief.""Muslims had the confidence and self-assurance to understand that once that principle becomes part of the collective ethos, people will recognize Islam's truth and enter it of their own will. Historically, that is what happened throughout the territories under Islamic rule and, of course, far beyond."
"As civilizations rise, mature, decay, and fall, similar or the same circumstances will occur and recur. Tolerance and letting-be will be replaced by persecution, which calls for force to re-establish religious freedom."
"At other times, the attitude expressed in: To you your religion, and to me my religion (109:6) will be more appropriate."
"The present is a period of the latter sort, one in which jihad is seen in our resolution, perseverance, forbearance, and devoted, patient preaching. And so we teach and explain. We do not engage in coercion, for there would be no benefit in our doing so. The misguidance and corruption of others is neither the target nor the focus of our efforts. We provoke, target, or offend no one. But, we try to preserve our own guidance in the face of misguidance. And in our own lives, we strive to establish the religion."
"Just because a particular Qur'anic command is not applicable in present circumstances does mean that it is no longer applicable or relevant. Rather, it means that the command can be applied correctly or properly only in certain circumstances. We do not know when such circumstances will recur, only that they will."
So there must be an orthodoxy button to push on and off, at least until the times are more appropriate? But hold on:
"Religious tolerance is, in some sense, a sociopolitical characteristic special to Islam"
"Islam also applies Muslim-specific deterrent sanctions to maintain the Islamic social order and ethos. An analogy may clarify this point. Most states have armed forces. These forces are composed either of volunteers or conscripts. Both types of soldiers are governed by the same disciplines (and sanctions). There is no "conscription" into Islam, for you can enter only by repeating the shahada.  To be valid and acceptable, this declaration must be voluntary and sincere. After that (converting to islam), the duties and obligations of Islam apply equally to all Muslims."
"Unsurprisingly, most breaches of discipline are slight, informal, and informally put rightusually by one Muslim advising a fellow Muslim to do the right thing and stop doing the wrong thing. Elaborating, exaggerating, or even reporting on someone's shortcomings or sins of others is considered a grave fault in Islam. Forbearance, forgiveness, patience for others, strictness for oneselfthis is the more commended and generally practiced stance of the overwhelming majority of Muslims."
"However, certain kinds of breaches threaten the social ethos as a whole. If such threats are not countered, the social ethos becomes eroded and society's general order and stability is undermined. Where informal private efforts to correct matters right have failed or are of no use, formal public measures, including force, must be applied. For example, Islam forbids the consumption of intoxicants, gambling, adultery, fornication, fraud, theft, and other harmful practices. It considers them both sins and crimes subject to punishment. If these vices are allowed to take root and spread, society has failed to fulfill its duty to the law and moral ethos of Islam."