As one VGC member from Saudi Arabia, a country with most strict religious observance, wrote that those verses could even be fine, if cited unmodified, I suspect the case was deliberately amplified to get free publicity.
A patch after release and maybe a sticker on the box warning people that could be offended to patch the game before playing could have been just fine, shipping new patched copies to countries with muslim majority first could have been even better and nobody would have been hurt...