Well. Let's break this down.
Andraste never said anything about Homosexuality, she was more about "Hey, these mages are being ****". the Chantry forms in Orlais, Orlais is about as sexually deviant as the old romans were IRL. The Chantry is in Orlais. The Chantry never outlawed homosexuality.
In Orlais homosexuality is accepted. In Fereldan, it's not outlawed, but people see sodomites as "odd". No, they don't go in depth, and they shouldn't.