Shaykh Yasir Qadhi:

Clerics and leaders who instigate Muslims to ‘defend the honor of the Prophet (saw)’ by attacking people who have nothing to do with insulting his honor, actually disrespect the memory of our Prophet (saw).

Yes, the movie was disgusting, but I’m sure the happiest person today is the person who made it, because his goal of smearing the Muslims has succeeded.

For how long will we tolerate such stupidity? (source)

Shaykh Abu Eesa Niamatullah:

I condemn it because the religion of Islam doesn’t allow such an action. Common sense and a call to revise sensibilities clearly have failed with such people. So we have to focus on the only thing that might speak out to them: their religion. These militiamen have not just insulted themselves, but they’ve insulted their Prophet, the same Prophet who stated authentically and unequivocally, “Whoever kills a person who is granted protection by the Muslims shall not smell the fragrance of Paradise even though its fragrance can be smelt from a distance of forty years of travelling.” (Source)

Imam Omar Sulaiman:

We are a people who hold all of the Prophets (peace be upon them) in the highest regard and it hurts us when their names are tarnished.

But we are also a people that believe that the greatest way of honoring the Prophet (salAllahu alayhi wa salam) is by following his example.

We cannot tolerate mercilessness in the name of the one sent as a mercy to all worlds. (Source)

Shaykh Faraz Rabbani:

Don’t defend the Messenger of Mercy and Beauty through #harshness and #ugliness. #Islam #Libya (source)

Shaykh Walead Mosaad:

Muslims in Egypt and Libya are mobilizing to condemn some obscure two bit “film” that was obviously made to provoke us, which it has succeeded in doing with an American consular officer killed in Libya and an Egyptian mob scaling the walls of the US embassy in Cairo yesterday. Unfortunately, we have become slaves to our passions and vices under the guise of religion, and we remain devoid of reason, mercy, knowledge, and wisdom. May Allah guide us all. (Source)

Dr. Aref Ali Nayed (Former Ambassador of Libya to the UAE, Member of the League of Libyan Ulema):

This is to express my deepest condolences to the families and friends of the late Ambassador Christopher Stevens and his fallen colleagues, and to the American people and government. I had the honor of personally knowing Ambassador Stevens, and witnessed, firsthand, in Benghazi and later in Tripoli, the care and hard work that he devoted to fulfilling his duties towards his country and towards Libya and the Libyan people. He was a man of dedication and honor, and I am shocked and deeply anguished for the loss of a dear friend and supporter of the Libyan people’s struggle against tyranny. Tyranny and darkness may wear a thousand guises, including pseudo-religiosity, but must never deceive us. Islam is a religion of peace and understanding, and Islam’s Prophet (peace be upon him) is the Prophet of Compassion. It is outrageous and totally unacceptable for criminals to kill and destroy in the name of defending Islam and its Prophet (peace be upon him). The criminals who committed this cowardly act must be rigorously pursued and rapidly brought to justice. May this tragic loss make us even more dedicated and determined to building our respective countries, based on the values of dialogue, understanding, and peace. (Source)

Imam Mohamed Hag Magid (ISNA):

“The Islamic Society of North America (ISNA) unequivocally condemns the killing of U.S. Ambassador to Libya Christopher Stevens, and his staff, and condemns the attack on the US Embassy in Cairo. Reports indicate that those who killed them did so as a reaction to a video depicting the Prophet Muhammad (peace be upon him) in a profane manner. Although we believe that this video is hateful and bigoted, this could never be an excuse to commit any acts of violence whatsoever. The Prophet (peace be upon him) is loved and respected by hundreds of millions of people across the world, and no one can take this from our hearts. No one should fall into the trap of those who wish to incite anger. The Prophet (peace be upon him) should be our example in everything we do, and even though he was attacked and insulted many times throughout his life, he always reacted with compassion and forgiveness, never with revenge or violence.” (Source)

Shaykh AbdulRahman Chao:

No crime justifies another. The bombing of the American consulate in Libya was a barbaric crime. The perpetrators think they are defending the Prophet (pbuh) and Islam. No, they are in fact causing problems for the Muslims. Worse, as America moves its warships and drones in position to target the killers, no doubt innocent by standers will be killed; their blood is on the hands of the same immature fools. And no, if you think that this post means that I am putting more importance on this than the Syrians or the Muslims in Burma, kindly put your nonsense away and Unlike my page. Save your emotional baggage. Right now, we deal with this and we must condemn each thing at its time. (Source)

The most ridiculous thing about these protests is that they are rooted more in emotions than in clear proofs from the Quran and the Sunnah. In the Seerah, an incident clearly speaks in favor of not using violence against those who slander and speak ill of Muhammad (pbuh). Long before his acceptance of Islam, Suhail bin Amr, an extremely talented and eloquent poet used to slander and verbally assault Muhammad (pbuh) with lines of poetry and prose. In the Battle of Badr, Suhail bin Amr was captured by the Muslims. Recalling his insults, Umar bin Khattab consulted the Prophet (pbuh) saying, “Allow me to pull out his front teeth so that he will never say anything against you after this day.” With full equanimity and mercy, Muhammad (pbuh) replied, “I will not make an example of anyone; even as a Prophet, Allah [might] make an example of me [in the same way].”(Source)

Habib Ali al-Jifri:

من يعمم التهجم على المسيحيين بأقذع الألفاظ في ردة فعله على الفيلم الهابط ينطلق من نفسية مشابهة لنفسية صانعي الفيلم (Source)

Rough translation: “We can’t say all Christians are responsible for this film because then we are doing what the producer did by grouping all the Muslims together.”

We condemn the murder of Ambassador Chris Stevens in Benghazi.
The responsibility of this heinous crime squarely falls on both the perpetrators and those who inflame the emotions of a people [to react] whilst they go through the labour pains of transitioining to a new and lasting positive change [in their country]. (Source)

Shaykh Yahya Adel Ibrahim:

Attacks on #US Consulate in #libya – Murder, Disgust, Sinful, Barbaric, Shameful, Ignorant & against every tradition that Islam Calls to.(Source)

Shaykh Yaser Birjas:

In response to the voilence erupted in Libya and Egypt and to the disorderly protest of the people there in the name of defending the honor of the Prophet s.a.a.w:

وَمَنْ أَحْسَنُ قَوْلًا مِّمَّن دَعَا إِلَى اللَّهِ وَعَمِلَ صَالِحًا وَقَالَ إِنَّنِي مِنَ الْمُسْلِمِينَ
“And who is better in speech than one who invites to Allah and does righteousness and says, “Indeed, I am of the Muslims.”

وَلَا تَسْتَوِي الْحَسَنَةُ وَلَا السَّيِّئَةُ ۚ ادْفَعْ بِالَّتِي هِيَ أَحْسَنُ فَإِذَا الَّذِي بَيْنَكَ وَبَيْنَهُ عَدَاوَةٌ كَأَنَّهُ وَلِيٌّ حَمِيمٌ

“And not equal are the good deed and the bad. Repel [evil] by that [deed] which is better; and thereupon the one whom between you and him is enmity [will become] as though he was a devoted friend.”

وَمَا يُلَقَّاهَا إِلَّا الَّذِينَ صَبَرُوا وَمَا يُلَقَّاهَا إِلَّا ذُو حَظٍّ عَظِيمٍ

“But none is granted it except those who are patient, and none is granted it except one having a great portion [of good].”

**How can good prevail, if we respond to evil by escalating it with an act that is even worse?(Source)

لِّتُؤْمِنُوا بِاللَّهِ وَرَسُولِهِ وَتُعَزِّرُوهُ وَتُوَقِّرُوهُ وَتُسَبِّحُوهُ بُكْرَةً وَأَصِيلًا

“That you [people] may believe in Allah and His Messenger and honor him and respect the Prophet and exalt Allah morning and afternoon.” al-Fath 48:9

It’s an honor to defend the honor of the Prophet, but it’s equally disgraceful to defame his honor in the name of defending his honor(Source)

Imam Suhaib Webb:

Normative books on Islamic law detail that representatives of foreign governments and their property should be treated with the highest respect. Instead of saying, “Why does Islam encourage this,” reality would dictate, “Why are some Muslims so ignorant of their own faith and ethics?”(Source)

Nouman Ali Khan:

The film is offensive because it misrepresents Islam. Senseless violence and murder is offensive for the same reason. (Source)

We shouldn’t be mad at haters. We should feel sorry for them. They can’t harm us. They can’t harm Allah’s deen. Just themselves. (Source)

Our messengers (S.A.W. ) honor came from the sky. No one on earth can take it away. (Source)

Tarek El-Messidi (Not a scholar but a student of knowledge and founder of Celebrate Mercy):

CelebrateMercy Founder Tarek El-Messidi stated, “When lies are spread about our Prophet, we simply respond with the truth. And the most effective response is to embody his merciful character on a daily basis. Violence and vandalism carried out in his name are more offensive than the content of any film. The Quran tells us that the Prophet is praised by God and His Angels; even a million films cannot threaten his status as the Best of all Creation nor his love in our hearts.” (Source)

I will update as I find more. Please comment if you do find more.