The official FAQ says that FileVault and FileVault2 are incompatible with Diablo 3. How can I install Diablo 3 on my Mac if my harddrive uses FileVault?
I wasn't aware of the issues with Diablo 3 and FileVault, but just confirmed that I have FileVault turned on for my primary HD where Diablo 3 is installed. One difference that I can tell between my setup and yours may be that I turned on FV after I had installed Diablo 3.
A few weeks back I installed a new drive in my Mac and the first thing I setup, after running the OSX Lion upgrade was to start the Diablo 3 download and install. It wasn't till a week later that I realized that I forgot to turn on FileVault and that's when I turned it on. So it could be that a way around the issue is to have FileVault turned off when installing Diablo 3 and then turning it on afterwards.
Blizzard's archive format is incompatible with FileVault due to its low level nature. To get around this problem, you need to move the installer to a partition that does not use FileVault. I would also recommend installing it to a partition that does not use FileVault as well, in case later game updates use the MPQ archive format as well.
I was able to use the following steps to get around this:
This allows you to keep FileVault enabled on your primary partition while also installing Diablo3. That is, you get the best of both worlds at the cost of creating a special partition for Diablo3. This way you do not have to disable FileVault for your entire computer.