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.