The paragraph you quoted and the one Elagabalus quoted are irreconcilable.  The church should withdraw and apologize for the implicit -- nearly explicit --  justification of violence in the paragraph Elagabalus quoted.

But here's the good news:  Very few people are aware of the existence of this or similar documents, and fewer yet take them seriously.  The church's teaching about homosexuality is untenable and most of the Catholic world is moving on, just as it did with the teaching about contraception.  Sooner or later, the pastors of the church will catch up; or not.  It doesn't make a lot of difference.