The intelligent design being advocated today hints that God is always tinkering with organisms, introducing "irreducibly complex" features and so on. The Cardinal is saying God set it all in motion, and everything unfolded according to the original programming He'd set up. So, no, the two statements do not contradict one-another.
I'd quibble, saying "frequently" (more so in the 'evolution' of the higher organisms).
First of all, I don't begin to see that in the above article, and secondly, where in ID theory or in RC theology does it require a belief that God (or the Designer) is always tinkering with Creation?
IMHO, God can do anything any way he pleases, and He occasionally and gradually allows us to understand how He accomplished some of his work. He could have set it in motion at the start and walked away, or he could be tinkering all the time. It does not matter one way or another in accepting the idea of a Creator.
For any but the most arrogant, the deeper the understanding of the sciences, the deeper the appreciation of His creations.