If 'seem like dark forces' is the best you can come up with, then it sounds like you're on no better ground than the theists.

It doesn't seem to me that they're "religion in scientific clothing", but rather an institution that cares about lots of big questions, some of which have traditionally been (and are still) answered primarily by religious sources.

You can't just excise a whole part of the human experience and not expect to lose something good. Diversity is sometimes far more valuable than optimality.