Morally heinous do occur across the globe, and it is of particularly great shame that such acts are sanctioned, even promoted by nation-states such as Saudi Arabia and Iran. However, it is important to make the distinction between moral failures as a result of cultural condition and moral failures because of inherent religious predisposition for violence.

I agree that oftentimes people tend to pick the "peace" surahs when describing the faith whilst completely glossing over the "sword" surahs that sanction holy war. Both must be understood to gain a greater comprehension of the Islamic faith. However, the Bible itself is often subject to the same cherry-picking (especially in the violence filled Old Testament) where people quote verses from Deuteronomy when arguing against tattoos but totally ignore the fact that slavery was permitted and the fact that the ancient Israelites committed a complete ethnic genocide of the indigenous Canaanites.

The moral failures you have described are more or less perpetrated by the governments of these nations, or at least by a ruling class of some sort. In these situations, moral failures arise not out of the inherently violent nature of the religion (although many facets of Islam promote retaliatory violence and the faith itself was founded amid the political realities of a war-torn peninsula populated by constantly warring tribes) but from the despotic tendencies spawned by the harsh realities of post-imperial rule. These nations have long been exploited by predominantly Christian European nations and, as such, cling on to anything and everything that would distance themselves from their subjugated past and their culturally-domineering overlords.

Religion is the starkest and most tangible identity that these nations can cling on, and the local despots who have risen in the power vacuum following decolonization have merely used religion as an excuse to keep their populations in check. Moral failures would have occurred regardless of religious affiliation (hence why political instability still reigns in many parts of Latin America and Africa, regardless of local faith). If the population had been any other religion but Islam (as was the case in the Belgian Congo and much of south-central Africa), other excuses would have been made to do morally heinous acts. The Burundi and Rwanda genocides saw the extermination of the Tutsi people by the Hutu- a demographic group of largely the same religious affiliation.

Proportions of numerical size are of little concern to this analogy. What matters is that both Westboro and Daesh are subgroups within their respective religions that have organized themselves and are well known for the extremist interpretations of their core religious texts.

Morally heinous people will always find a reason to justify their morally heinous deeds- it is only a true pity that many of the nations that suffer beneath unjust despotism share one confession of Islam or another. But make no mistake- placed in the exact same conditions, the same burdens of imperialism, colonialism, and economic exploitation, the countries you have mentioned (Saudi Arabia, Iran, Pakistan) would have been very similar to what they are now even if they were Christian, Jewish, Buddhist, or any other religion. Even religions of peace, such as the peace professed in some portions of the Abrahamic faiths and common in Axial Age religions, can be led to violence by morally heinous people in defiance of the tenets of their faith; the deplorable case of Buddhist extremists and the expulsion of the Rohingya in Indochina attests to this.

EDIT: In the interests of full disclosure and in avoidance of conflicts of interest, I'd just like to say that I am not attempting to justify the morally heinous actions of tyrannical individuals of the Muslim faith, or any faith, nor am I Muslim myself.

TL;DR: Bad people will find reasons to do bad things, and religions aren't the source of heinous acts but a convenient excuse for evil people to do evil deeds. To generalize an entire religion as innately violent due to the unjust behavior of extremists groups and despotic governments that arose from secular causes is flawed and inaccurate.