Now that I've ansered all these questions, I have one for you that you never answered... Why wouldn't you just delete the application rather than revert the system?
You are right - I never did answer the question. It is the way to go. I don't disagree. But when you brought up the fact that your drive can crash, I implicitly began exploring on to that topic. My bad.
The TM should handle any scenario for me short of the intenal drive crashing. But there are several folders I don't backup to TM, including:
~/Applications
~/Downloads
~/Dropbox
~/Music/iTunes
~/Movies (don't want to copy 4GB movie rentals)
and my Parallels virtual machines.
Something I didn't mention before, I do have a Mac Mini and that will keep me going until the MBP drive is replaced, in the case it completely fails. Since there is a 2nd computer, I don't really need the ext drive for a bootable device. But, I do think it is good as a catch all. Meaning, what ever isn't backedup via time machine and will be copied to the clone, just in case I did miss something with TM backups.
Is it possible to restore just certain files from the clone using CCC? The scenario for me would be, pick a date in TM and restore. Then what ever is missing, restore from the clone. Or is this overkill and there is a better way?