I hate it that whenever I make a change in Xcode 4 it automatically does a "Git add" command. Is there a way to make this stop?
No. Xcode 4's git integration is "broken" in that they tried to present a uniform interface to source control regardless of whether the back-end is git or svn. That means they're supporting only the lowest common denominator of functionality. As a result, use of the index (the "staging area") is out. It always does auto-adds no matter whether you want it to or not.
EDIT: Actually, I don't think it auto-adds. I think it always does commit -a. Looking at git status on the command line shows me many new and modified files that are NOT staged. But I'm sure if I committed with Xcode they'd all end up in that commit.