Yes, religion is by definition irrational. Humans generally aren't very rational beings. Love is irrational, it makes us do irrational things, but I'm sure we can agree, on the balance, love is a good thing. Thus dismissing religion on irrationality grounds is not very meaningful.
I also didn't say we should dismiss religion because it is irrational, I said people who were religious were irrational. I believe that still stands.
If anyone asked, I would say we should dismiss religion because it is harmful. Harmful to our stability, harmful to our advancement, harmful to the people that follow it and harmful to the people stuck in it against their will (either country, family or society). Today the negatives of religion far outweigh any good it can do. There was a time and place for religion, but we have outgrown it.
The Middle East isn't solely a religious conflict, it's very much an ethnic one as well. Oppressive countries are oppressive, they're not liberal countries that just happened to read in a book that they should kill and maim those that worship in the wrong way. Closely knit groups (families, societies) are going to sanction deviators regardless of religion.