Carbonite keeps a record of all files that it ever tried to back up, so even when you make the backup set smaller, your Carbonite Backup Index stays the same size. (The Backup Index acts as an archived list of the backup set; file names, locations, metadata, when files were editted, etc). When these indices are extremely large, it's tough for the CarboniteDaemon to read them, which ramps up the CPU.
[I'd also like to note that the ~/Library folder contains thousands of cache folders (some of which, Time Machine doesn't even bother backing up).]
The best way to make sure Carbonite doesn't hog your CPU is to do the folllwing:
1) Delete the backup on the Carbonite servers (you'll need to send an email to customer care to do this).
2) Once you get confirmation that your backup was deleted, log into the Carbonite website and click "Install"
3) During the installtion, [this part is *ESSENTIAL*], select >>> "I'll manually slect what to back up later", then click 'Next' and complete the install.
4) When the Carbonite prefernce pane opens, click the 'Backup' tab and navigate to your home folder, then select your files and folders that you want backed up. [do NOT, I repeat, DO NOT back up your 'Applications' folder... since each time a file is opened/editted, Carbonite flags that file for backup. This means that if you select a .app file, every time you open the application, Carbonite will try to back it up > killing CPU]
5) I recommend that you go through the Library folder with caution and only select *files* (not folders) you know you need > do *not* just select folders that you recognize the names of.
(You can also call customer care to assist with this process, but keep in mind, these are files on *your computer*, so if you don't know what it is, then it's likely the representative that assists you won't know either.)
And, I agree with you, I wish they had done more intensive software testing to catch issues like this before it was released.