Yes, they've done that in the past. It wasn't right of them, and they've made reparations and/or apologies. I don't think it's proper to assume that the Church would make the same mistakes again.
Humanity and its leaders are surprisingly predictable in making the same mistakes over and over again. The key thing to remember is that, with UGE and Goblinazation, we no longer had race being defined as skin tone, but as fully expressed genetic differences. I don't think all, or even most, of the Church believed this to be the work of the devil, but a single person in authority? That
is possible, and can be devastating when his opinion can enforce his group's agendas.
Even recently, I've seen things in official sources that just don't quite jibe with what I know. The entry in Street Magic on "Christian Theurgy" brings up things that, while they may be okay in other flavors of Christianity, just don't work for Catholicism. (My wife is going to be playing a Catholic magician, and the tradition she came up with is uses the multitude of saints as manifestations of spirits. She's eventually going to have her character join a monastic order to get her initiation.) I don't know if any other books in the new line-up mention the Church; feel free to point out any other references that have turned up.
Well, there is basis in the Sixth World that the Catholic Church is a "player" on the world stage. They might not be as powerful as some AAA Corps or the "first world" nations, but they aren't that far out of the loop. Regarding the Christian Theurgy tradition, I believe it was created on the basis that (as it says in its entry), most Christians do
not believe that magic is divine in nature. So it's a bit more mixture of Renaissance ideals regarding magic and Christian study. Now, I think her creating a tradition based off spirits being Saints and such could be based off a group of Christian magicians that
do believe that magic is divine, and the power they wield comes straight from their God/beliefs. This is why I like the new magic system with flexible traditions, it allows the players to come up with some great new ways to do old tricks.

As far as future books, since some factions and such regarding the Church were in previous books detailing "conspiracy" books, I wouldn't be surprised to see an entry or two in the upcoming
Conspiracy Theories sourcebook due out this year.
'Course, the things that have been brought up are making me consider staging a run requiring the group to sneak into the Vatican (physically and/or virtually). I might have to re-watch MI:3 just to get an idea of where to start with the security measures. Heh.
Another good one to check out is
Angels and Demons, based on Dan Brown's book. It gives you a great feel of how the "hidden" Vatican may look/operate.