We're just not as evolved as some people think we are.
If we look at the ****** kingdom, there's a one main reason why ******* of the same species ****/****** eachother, power. This can be divided in several sub-reasons, which are (& I might miss a few).
1. The right to mate
2. Territory
3. Prevent other's offspring to reach adulthood
We humans have added a few sub-reasons, but it's still about power.
1. The right to mate (remember the Trojan wars?)
2. Territory (speaks for itself)
3. To **** other's offspring (don't think we still do that on purpose, but it might still happen subconsiensely (SP?))
4. Economical/financial power
5. religious power (although religion is often just used as an excuse)
As you can see, thanks to the fact that we've evolved a bit further than most *******, there are more things that are precious to us (I won't see a chimp fight over a lump of gold... I can however see two humans fight over it).
In general, we fight because we want to stay in (or get) power, just like any other ****** & unless we become aware that we're acting like ******* & want to change that, nothing will ever change, except maybe survival rate of the human being, since I've never seen a chimp fight with guns & nuclear weapons (another improvement that we could only have achieved because of evolution).
This case is no different. The religious leaders in Afghanistan see this man as a threat, because more people might follow his example (even though it is unlikely) & they'll lose their power base. The only option is to eliminate him.
Of course we all disagree with it, but we're not the people in power over there (in Afghanistan).