No, the Jesuit concluded that the aliens and their world must be the product of Satan because they had what appeared to be a perfectly moral society but without any knowledge of God. This directly contradicts the view that all knowledge of right and wrong comes only from knowing God.
(He was later disabused of this notion by none other than the Pope, who pointed out that this reeked of the Manichaean Heresy.)
The Lithians did not merely cease to exist: their planet exploded. Most likely due to human mining efforts, but the priest was conducting an exorcism at the time, so it's perhaps a bit ambiguous.
I don't remember the second book very well--I should really order copies of the whole tetralogy--but the last 2 books, Black Easter and The Day After Judgement, are also very thought-provoking.