According to the Daily Mail, former Vatican astronomer Fr. George Coyne was in fact sacked because of his opposition to intelligent design.
However one must be careful in reading British articles about the topic, as it appears that a more generic, abstract definition of "intelligent design" is meant here, rather than the "intelligent design" of the recent U.S. controversy.
What Fr. Coyne's nemesis, Cardinal Schonborn of Vienna, is arguing, according to the article, is that there is a divine purpose and design to nature. Coyne argues that God is not constantly intervening, and that we need to move away from the notion of a designer God. He argues that God should be seen more as a parent or someone who speaks encouraging and sustaining words — i.e. not someone who designs, but as someone who coaches.
The argument, then, is between viewing God as a designer, versus a kind of partner who lets the world do its thing with some moral support from him.
Intelligent design in the U.S., as I understand how it was recently argued, has been closely associated with Creationism. (The first intelligent design book was Of Pandas and People; in drafts, according to Wikipedia, "the word 'creationism' was subsequently changed, almost without exception, to 'intelligent design'".) The pope may be advancing a more nuanced version of it. On the other hand, he is saying precious little about it and probably will continue to say precious little. It seems to me he is highlighting one or two crucial points which, while tantalizing, don't nail down a particular belief. And that may be as he wishes. It is clear he cannot accept the atheistic evolution the scientists demand, but with the sullied reputation of intelligent design, he has to be careful.
It should be interesting to see how this plays out.