The "God of the Gaps" is an argument that, since there are things we can't figure out, there must be a God that did it. I think of it as an argument for people who don't think God could do something outside the limits of their imagination. This isn't what the Catholics do. They believe there is a God that created all things, and hence the laws of nature were God's doing, and evolution was God's way of creating species. They don't use evolution as an argument that God exists.
The "God of the Gaps" argument is more a fundamentalist Protestant argument, where they pick away at evolution until they think they've found a fatal flaw with it, and then say that proves God did it. Even saying that evolution is compatible with Christianity (which the Catholics have said for a long time) removes the God of the Gaps argument.
In your last paragraph, you fail to provide support for Catholic doctrine being at odds with scientific theory. You provide examples of the Catholic church saying some things are immoral, which is not a conflict with science. The use of embryonic stem cells could be immoral even if it's scientifically useful (consider some of the Nazi experiments on Jews in WWII for a parallel). Contraception could have lots of demonstrated benefits and still be immoral. The church can tell people to do things one way because that's the moral way, while knowing it isn't going to work in almost all cases. You and I don't agree with those moral stances, but they aren't anti-scientific.
Removing all the cases where the Church says something is possible but immoral, you have one stupid statement by a Pope in 2009. I don't think that comprises evidence that the church is anti-science.