The pope is not in favor of separation of church and state. Opus Dei is a conservative organization based on Spanish catholicism (Where many in the hierarchy supported Franco and the fascists) but, like other groups, cannot be evaluated wholly on the basis of the views of its founder. As a whole, its tenets are supported by the Church hierarchy.
We do not hold those views in most western democracies- although the "Under God" pledge is (I feel) undermining the separation.
Opus Dei must be assessed as an organization under the umbrella of the Catholic Church, its founder beatified by the hierarchy. I cannot agree (atheistic or at best a tree-hugger) with the tenets of the Catholic Church or any church, but misinformation such as that posted by mesophist spawns intolerance.