First things first:
getting to know the context

Al-Bouti was one of the most prominent figures of Islam Scholarship during the 20th and 21st century.

His core competency was “Quranic Sciences”: understanding the revelation, that affects all the understanding of Islam.

It is a heavyweight knowledge, it requires mastery of arabic, superior analytical skills, vast knowledge of history, and deep knowledge of prophetic narrations (which is equivalent of more than 20PhDs).

I have listened to many things, not everything, from Al-Bouti’s work, but all the lessons I have heard from him, made my heart grow fonder in the love of ALLAH, and he showed me a high level of humility and Taqwa, that I couldn't feel before.

Listening to Al-Bouti’s work made the connection, and made me get to more concrete understanding of Quran, and of the knowledge of ALLAH, more than any time before

Al-Bouti was criticized in his last days for being pro-Assad-Regime, who was oppressing civilians during the Syrian manifestations, which turned later into a revolution, which turned now into a total mayhem.

The “Fitnah”:
the split of opinions that created a bloody conflict

Unlike other Islamic Scholars who supported the rebels in Syria, Al-Bouti was:

• Syrian, he knows the Geo-political landscape of Syria, and the social culture of its people, and have seen other revolutions unfold.
• Close to Bachar Al-Assad (The Syrian tyrant), he knows the man more than anybody else, he knows the regime.
• He was close to diplomatic relations and public policy makers, he knows the implication of actions undertaken or words spread.

and mainly:

• He was a man of the Quran, and a true muslim must know the weight of wisdom of the Quran, especially in decision making.

In other words, we shouldn’t be quick on judging his position, he surely have his own reasons and rational arguments that he is convinced with.

1- Understanding Priorities:

In Islam there is a science called “wisdom of priorities” and in such a conflict, virtues and actions must be postponed later till the foundation is ready to handle the new virtues.

When ALLAH gave the Qiblah example in Surat Albaqarah (direction of prayer)

The foolish among the people will say, “What has turned them away from their qiblah, which they used to face?” Say, “To Allah belongs the east and the west. He guides whom He wills to a straight path.” (in Arabic here)

ALLAH ordered the muslims to pray in the direction of Jerusalem, then after 13 years of revelation, ALLAH commended that muslims should change their Qiblah, and start praying definitely towards the Kaaba in Mecca. Then some jews and christians in Medina(not all of them) started criticizing the muslims for changing prayer direction from Jerusalem to Mecca.

Why Did ALLAH do that?

For sure it has many wisdoms, but one of them takes into consideration that there were many converts, from jews and christians, they used to pray towards jerusalem. During the night of “Israa-and-Miiraj” , prophet Muhammad (SAW) prayed with all the prophets in Jerusalem. Jeruslem was the Qiblah for more than 13 years.

Praying towards Jerusalem was a transition step, that was not only made converts familiar with Islam, but also showed the Jews and Christians “we are just like you, we got the same revelation, from the same God”, it was not alienating for many jews and christian started converting to Islam.

This made Islam melt with the cultural patch, and it strengthened them in Medina, and they integrated culturally with other religious communities.

When muslims were exiled from Mecca, 17 months after settling in their new city Medina(Yatrib), where Islam changed from a shy community to a world movement, ALLAH made them change the Qiblah towards Mecca, it was preceded before by the revelation of the Legacy of Abraham. Where ALLAH explains the origin and purpose of Islam as it was pioneered the first day by prophet Abraham. Announcing that the Kaaba should be the new and final Qiblah for the muslims, clarifying that this change will distinguish between the true muslims who follow the words of ALLAH by the letter, from those who just stick to tradition without questioning their inherited believes and personal opinions.

If Mecca was decreed the first as a Qiblah, Islam will have so much resistance in getting to be accepted by the people. Instead, ALLAH made the first prayer in Islam prayed in Jerusalem, then he made Jerusalem a Qiblah. Hence, the people of the book (jews and christians) were more open to hear about the teachings of Islam, Medina become more united as a city and as a diverse community, then ALLAH tested again the hearth of the faithful by declaring the new Qiblah

Qiblah transitioning is a highly important event, it showed prioritized the “Why” over the “How” in Islam.

It shows us that integrity of the ethics are more important

Al-Bouti knew that there is a deeper problem within the Syrian Society, social bonds and trust between people, and that a revolution will destroy the country more than the current regime… keeping his priority cards on the table

In his speeches (which can be found on youtube) were not supporting the Regime or asking for allegience, but he asked that ALLAH guides the regime towards the straight path and that people do a smooth transition and call for conversation and discussion rather than one-way accusation.

2- In case of doubt, Muslims go back to the prophetic tradition.

Mankind was [of] one religion [before their deviation]; then Allah sent the prophets as bringers of good tidings and warners and sent down with them the Scripture in truth to judge between the people concerning that in which they differed. And none differed over the Scripture except those who were given it — after the clear proofs came to them — out of jealous animosity among themselves. And Allah guided those who are faithful to the truth concerning that over which they had differed, by His permission. And Allah guides whom He wills to a straight path.
Quran — Chapter of Albaqrah(2) — verse 213

Conflict and divergence of opinion is as essential as existence itself is. Prophet muhamad peace be upon him, himself couldn’t agree all the time with his companions, and had divergent opinions, until the revelation came each time to fix difference of understanding.

In the case of any conflict or misunderstanding between muslims, we call for the prophet to show us “the right choices”. Else, why would ALLAH send a prophet in first place.

But no, by your Lord, they can have no Faith, until they make you (O Muhammad SAW) judge in all disputes between them, and find in themselves no resistance against your decisions, and accept (them) with full submission.
Quran — The Chapter of Women (4) verse 25

But, in the case of Al-Bouti, and the Syrian regime, there wasn't anything in Muhammad’s history (SAW) that showed what should be done in this conflict. To get the just answer, and find truth, we should follow not only what prophet Muhammad (SAW) used to do, but also what he was “Ordered to do” by ALLAH, and this can only be found in the Quran.

And We gave to Abraham, Isaac and Jacob — all [of them] We guided. And Noah, We guided before; and among his descendants, David and Solomon and Job and Joseph and Moses and Aaron. Thus do We reward the doers of good, And Zachariya, and John and Jesus ….. They are those whom Allah had guided. So follow their guidance. Say: “No reward I ask of you for this (the Quran). It is only a reminder for the nations”
Quran — Chapter of Al’Nam- verses 82–90

Prophet Mohammad (SAW) was ordered to follow the guidance of the prophet before him, and in this exact situations was encountered by prophet Moses (Peace be upon him). Following prophet Mohammed means abiding by the decision made by Moses.
Indeed, Prophet moses faced a much worse situation along with the children of Israel. but ALLAH told him.

And [recall] when We saved your forefathers from the people of Pharaoh, who afflicted you with the worst torment, slaughtering your [newborn] sons and keeping your females alive. And in that was a great trial from your Lord.
Quran — Chapter Albaqrah (2) — verse 49

Even with the bloodshed that Pharaoh did and super tyranny he had, and over powering his people. ALLAH did tell to Moses “to tell him gentle words and to debate with him and discuss with him”.

Go, both of you to Pharaoh. Indeed, he has transgressed. And speak to him with gentle speech that perhaps he may be reminded or fear [ Allah ]
Quran- Chapter Ta-Ha (20) — verse 43–44

and I thing that’s a wise way to go with tyrant oppressors, debate first, convince first, and at the same time build down the foundation. Going through an unplanned revolt is just foolishness we read through recent history that only brought destruction to its people rather than peace.

Conclusion:

A man, whose last words were Quranic Sciences teaching, who always asked for tolerance, who is loved and adored by the Scholars themselves, who left this life martyred with a Quran in his Hands, dying in a mosque. Recorded for all the world to see it, and the generations to come to witness that Al-Bouti was Martyred. InchaAllah.
ALLAH would not give such a high prestige and esteem to him, as he has given the same prestige with a similar martyrdom to the great companion of prophet Muhammad Peace be upon him Uthman bin Affan.

Narrated Uthman bin Affan: The Prophet said, “The most superior among you (Muslims) are those who learn the Qur’an and teach it.”
Source: Sahih Al Bukhari, section 61 on the virtues of quran, quote 546

Al bouti’s position can be explained and is debatable, but it does not make the man a traitor or an evil being, he just had his own opinion on a difficult decision to take.