I think we would only be differing in how much of threat ISIS is, and probably not by much.
What are these “violent cultural tribes”?
Perhaps if we knew what we’re supposed to be comparing ISIS to, we’d be able to answer better.
OP: People care about ISIS because they threaten oil security. If they didn’t they’d get about as much attention as whatever fucked up shit goes on in Africa.
No one knows what you are talking about. Which specific “violent cultural tribes” are you referring to?
The reason these violent tribes (I assume you mean hunter-gatherer cultures) still exist, in places like the Venezuela-Brazil border, is because those places are remote and difficult to access, govern and police. What do you want the governments of Brazil and Venezuela to do, exactly? I think both of them have more pressing challenges on their hands right now.
These tribal atrocities are happening in countries with a government and armies to keep them in line. The international community should condemn the atrocities but whatever government is in charge should keep their warring tribes in line.
As far as Isis, we should help our allied countries in the region, but THEY should be the ones to snuff out Isis. This should not boil down to or be seen as Isis vs. Crusaders from the West. It gets them all kinds of support.
“Isis” is the Egyptian goddess. 
First of all, you need to demonstrate that these “violent cultural tribes” are really still violent, and the level of violence found in the early anthropological studies cited by Pinker still exists. Most of these tribes are now in contact and under the control of national governments. Murders and violence will generally be reported to authorities and if possible the culprits will be prosecuted. Violent cultural practices are not allowed to “continue to exist” to the extent that the authorities can prevent them.
You also haven’t explained what you mean by “continue to exist.” Do you mean genocide, or do you mean changing their violent cultural practices? If the former, that’s clearly unacceptable. (Genocide as such against ISIS supporters wouldn’t be acceptable either, though military actions will be required to bring ISIS under control). If you mean the latter, as I said above these cultural practices are not still permitted or tolerated among groups under government control.
The premise that primitive tribes are somehow comparable to ISIS fails on all levels. You might as well ask why we still allow the Mafia or violent drug gangs to exist.
A nit pick: these cultures are not hunter-gatherers, but subsistence agriculturalists.