Let me clear a few things up:
This is like going to a gourmet restaurant and demanding to make your own food in the kitchen and next to everyone else's meals.
FileVault is driver-level encryption Apple has added as a basic feature in its operating system. It's powerful, extremely effective, and perfectly transparent to the user and any competent developer. It's not a 'program' - it's an integral part of the OS.
To use FileVault, programs ask the OS to read and write whatever data you need to whichever volume you wish to use. The OS will do so, in compliance with the UNIX permission system. (Ever wonder why malware is so rare on Macs? Look no further.) The only way you could run into problems is if you're arrogant enough to write your own file-access routine that tried to circumvent the Apple filesystem and drivers. Apparently Blizzard has done just that (with DIII and now with WoW). Beyond frustrating, this scares me.
This means Blizzard's programs (which ask for UNIX root password during installation) are doing direct filesystem writes. This is fundamentally NOT cool.
Look, I'll be blunt: I do NOT trust Blizzard to know what they're doing writing directly to my filesystem and hacking around my Apple-provided system-level protections against stupid developers. (Note: this is exactly what malware typically does in windows to bypass anti-virus software. It should be noted that I've reinstalled WoW a dozen times because the software destroys its own install. During this time I've never reinstalled Apple's OS X for any fault of the OS.)
Blizzard borrows your front car key and feels that's permission to go play with the wiring in your Ferrari.
Writing a game (or any program) that so blatantly bypasses system-level services in an advanced operating system is sloppy, amateur, and unprofessional. Blizzard can do better and we as users should demand it. Ask yourself who's smarter, the guys writing at Blizzard or the filesystem engineers writing the filesystem behind iPhones, iPods, iPads, Apple TVs and Macs.
As far as why they did it- I suspect something like this, please correct where I'm wrong: Blizzard has to make game files that are larger and be accessed faster than the crap file system in Windows can deal with efficiently. Therefore they created their own micro 'nested' filesystem (MPQ) to do it. (This is just like what Killer NIC's do for the IP stack; Windows' TCP stack sucks.) This MPQ system has been cross-compatible for years. But now, Blizzard decided to unify the code-base a little and that means doing direct drive writes instead of going through the OS. Our OS doesn't suffer the problems, but we have to deal with Blizzard potentially damaging our filesystem by its ham-fisted attempts to write to HFS+ as if they know what they're doing.
I'm a WoW player, I'm not impressed with DIII - and certainly not enough to deal with this crap. SCII isn't even on my radar because of it. I'll focus on developers who know their place and don't go messing under the hood when they ask to borrow my keys.