How do you deal with a problem of this kind?

When you have men driven and powered by their faith and zeal that they are fighting not merely a righteous cause but is in fact a DIVINE one:

http://www.aljazeera.com/news/africa/2014/06/dozens-killed-fresh-nigeria-attack-20146516155739408.html

then whatever they do is blessed.

And they will press their case to the only logical end point - the utter destruction of their enemy - the INFIDEL.

Question:
How would you solve such a problem?

Answer:
This is one that was shown to work.
When Hulagu Khan, son of Genghis conquered Mesopotamia and now ruled from Baghdad, his troops, now patrolling the urban districts. Now and then, they were ambushed and a Mongol soldier or two could be killed.
For this offences, everyone in the district that killed a Mongol soldier - man, woman and child, was put to the sword at once. There was no trial before a jury of one's peers.

Very soon urban assaults on his troops stopped.