Most religious persons are, and i hope i am, rational persons. Even when considering the posibility of a spiritual experience i can tell who is crazy in a very long range of religion statements. (The tricky question is who is not, but that's another matter).
There is some forms of telling what is insanity, there is psiquiatry, but also you can see it looking for several aspects related to behavior. The same happens with love. Love is not per se madness, but it is not uncommon to see people who put love in to such dimension.
Religion is an easy hotspot for crazy people like the one you mention, it provides the source of authority they need to back up their anger and frustration. Now, i can tell there is some other form of fanatism very secular too.
I really don't think intelligent life in other planets would change my current point of view of the universe. I am counting with it. If there is a place for a group of religious persons who are not dumb to think of aliens being angels or demons, put me there. In anycase, from a more objetive point of view, abstraction is always the key to adaptation in any system of ideas.
Now, i would expect:
-The concept of human race grown (just because identity is build based in an other).
-The need for a human citizenship
-New form of racism (well specie related).
-A lot of new concepts, a lot of unique words and ways to think that might be strange to us.
Did some edit for bad english and some ideas. An interesting topic :)