The simplest remedy is to replace the fundamentalist regimes with secular regimes -- the Ataturk solution. The Arab man-in-the-street has no real reason to hate Jews or Christians, but is incited to fanaticism by the mullahs and imams. It is this leadership class that must be eliminated with extreme prejudice. One of the few points on which I agree with the NSDAP regime is on the issuing of the "Commissar Order"; just replace "commissar" with "fundamentalist cleric" and the thing could be used verbatim.
The only twist I would add is to have the offending clerics stoned to death by women -- preferably college-educated.