The cross is still there, and of course so is the church although along with the rest of Macau it's been given a nice fresh lick of paint. Here's a recent snap taken on my last trip at Lunar New Year looking towards the Biblioteca in the background.
Yes, that is the bell tower of the Carmel Church behind Isabella Wong. Notice the curved bits of concrete at the bottom of the picture? Well, these are just a bit of decoration that cover the small slope leading up to the church - I believe the place is actually a small park but its name eludes me at the moment.