Many scriptures in different religions (not only islam, but also buddhism) might be understood wrongly nowadays. The real intention might have been very diffent than the scripture reads literally.As far as I am concern the real issue is not what so called Buddhist, Hindus or Muslims doing.
The problem is the indoctrination.
If the scripture promote violence it is very difficult to avoid it.
For example the Dalai Lama claims: "The real meaning of Jihad is to fight and overcome ones inner enemies." In Buddhist view those enemies are: greed, hate and ignorance. HHDL thinks, the true islamic teaching is quite similar to that view.
Also in Vajrayana, the so-called wrathful dieties are angry against everything that hinders the dharmic progress: hate, greed, envy, arrogance, ignorance, and the 10 unwholesome deeds... They are not thirsty for blood, even if it is stated literally in the scriptures. Wrathful dieties seem to be wrathful, but they are nothing else than full of compassion.