It's based on the concept of striking first and asking questions later. It's not like they're going to listen to anyone after this anyway. It's human pride: A nearly universal human fear is the fear of being wrong, and it'll be a huge blow for them and their faith if it turns out their reasoning was flawed. A lot of companies don't sell their stuff to the Middle East anymore; I'm surprised Nintendo is that bold.
However, try to cast aside as much of your ethnocentrism as you can. Saudi Arabia is a very religiosly devoted country, much more so than North America and Europe. We have "separation of church and state"; the church IS practically the state there. It's not like this is going to start an outrage there...maybe only among visitors who bring in their GBAs and DSs with Pokémon games in them, which is very odd that they singled out this series and not anything else. (It also took them a decade to see this...What happened? Did Abdul Ali al-Abdul Ali see some kid playing it on the streets last week?)
This is no doubt something Nintendo did not want to hear, but the Middle Eastern market for electronic gaming is a very small one. (Bear in mind that Pokémon had already been banned in Turkey, though for entirely non-religious reasons. Also bear in mind that, when it comes to Catholicism, the guys at Vatican publicly announced that there is nothing morally wrong with Pokémon, but if anything, it fosters friendship through its link features and encourages compassion for all living things.)
Oh well. At the very least, that means I'm keeping my Afghan Machoke I got oer the GTS.