Crimes are not committed by groups but by individuals. Such individuals may claim to act with the authority of the group, but unless the group in question in fact has legal authority or responsibility for the actions of its members, only the individual can or should be prosecuted. That's pretty consistent with libertarian philosophy.
To begin with: "religion" is not a monolith. There are many religions, all with differing belief systems, whose members are legally responsible for their own actions.
Now to your examples: Jamestown? I think you meant "Jonestown", but fine - here a maniac and his demented followers killed themselves (in a foreign country, and of their own accord). A terrible thing, but no one has ever suggested that these people were in any way representative of anything resembling a mainstream or even offshoot religion.
Waco? Ask Janet Reno who created that nightmare. She'll lie to you, but it was her Justice Department, not the "cult" that turned a standoff into an inferno. Of course, she also snatched a little boy from his father and sent him back to Cuba, but hey, all in a day's work for the worst AG we ever had. Nixon's AG John Mitchell couldn't hold a candle to her for pure evil. In any event, this was in no way an example of "religion" but of a nutty cultist who apparently violated laws and might have been peacefully apprehended but for the stupidity of the government.
Pedophiles in the clergy? Now here's a better example. But when is this something condoned by any religion? (Islam, maybe, but let's not go there). Did they sometimes ignore it even though it violated not only the law but their own doctrine? - yes. Is it still an individual crime: yes, but so is the act of letting it happen. The "Church" did not turn its back - individuals within the Church did so and as a consequence, convictions have been obtained and restitution paid to the victims. What made it possible to punish the guilty: laws against pedophilia. Can libertarians at least support that?
As for guns: you're making the same argument from false premises, relying on the logic of liberal gun-grabbers. Weapons do not commit crimes by themselves; people do. Weapons may be used for legal, defensive, and constructive purposes or for illegal, offensive and destructive ones. Drugs like crack cocaine are different - they have no legal, defensive or constructive purpose; they just kill and destroy. Banning these drugs no more invites a "slippery slope" than banning individuals from owning thermonuclear devices - no good can ever come of it.
I don’t see the straw man arguement at all. His analogy seems good - religion like drugs (or pornography, gambling or substitute most any of the “vice” crimes that social conservatives love to rail against) can result in a great deal of harm to innocent 3rd parties. However, not every (or even most) individual application of it results in significant harm... not even to the individual choosing to practice it. We don’t make one illegal, why should we make the other? Again in both cases we CAN punish the actual ACT’s which do cause harm to others rather then the ACTs which simply promote conditions which MAY or MAY NOT drive individuals to commit harmfull acts to others.
Thus we can punnish the act of shooting some-one for drug money without punnishing the act of taking drugs just as we can punnish the act of shooting reporters and U.S. congress men or poinsoning children (Jonestown) without punishing the act which facilitated them - religious worship.
If you don’t like his particular examples, history is rife with examples of harm percipitated by religion. Let’s see. off the top of my head: 9-11, The Spanish Inquisition, The Salem Witch Trials, the Troubles in Northern Ireland, The English Civil War, the reign of Henery VIII th, The Programs against Jews in medievil Europe, The Childrens Crusade, The trails against the Knights Templar, The Muslim Conquests of the 7th-9th centuries, need I really go on?