What sort of agenda did you think the movie had? I suppose there's a slight humanist agenda, since it portrays nearly all the characters pursuing goals that probably aren't considered the ideal religious goals.
The thread of conservative vs progressive cardinals and factions goes through the whole movie, but the ending is the most "agenda" part (although handled subtly).
The ending reveal doesn't even fit neatly into the hot-button American political issue you're associating it with. The film is clearly trying to make the viewer work out their view on the issue, and I think the film takes essentially no stance (unless you think that not taking a strong stance in one direction constitutes endorsement of a different direction).
Some might even say the film lacks courage, both by taking no stance on the issue and by presenting a scenario that only vaguely matches the hot-button American political issue.