I'm not sure why something like that would "rock" anyone's faith.
God's plan was for Jesus to be crucified and die for our salvation. Judas was part of the unfolding of that plan. The Apostles, in their human nature, saw Judas as a betrayer, so that is what they wrote about, that is how they portrayed him. But I can very easily see how Judas can actually be seen as the catalyst for the crucifixion/salvation story. It doesn't change the ending, which is the important part...that Jesus died for our sins.