The Git4Idea plugin automatically adds changes to the index even with the improved git support in the new Intellij IDEA version 8.1.
There's even a post on the Jetbrains forum about this issue without any replies.
According to Embracing the Git Index Linus Torvalds once said "If you deny the Index, you really deny git itself."
If you want to use Git the way it was meant to be used you have to disable the plugin and revert to using git as an external tool or from the command line.
How are you dealing with the quirks of the abstracted git interface?