"For many, the Pope is a connection, or at least a representation of a connection to that which is of the highest order in the universe. Are we to belittle that? Trash that?"

Why not? If there is truly the "highest order", should it be above scrutiny? If we cannot poke a few holes, than we have created a sacred cow and not a true religion.

The pope is a man, not a deity. The Dali Lama (I've never been to his deli) is also just a man. They do good work, as do others. They are not above any of us.

" Are we not then merely demoralizing ourselves? "

Not at all. Blind faith and failure to question results in the ills of the world.