MacOS – safely remove /usr/bin/java from Mountain Lion 10.8.2

git is installed by Xcode. I doubt you'll have any problems if you replace it, but I can't give you a definitive answer to that…

1. What I'd do is rename the old /usr/bin/git to git_old, then rely on your path to select the new one.
2. If that doesn't work, move the new one to /usr/bin. I doubt Xcode is picky about which version of git it's using.
3. If that still doesn't work, move git_old back to /usr/bin/git and use either a direct path, rename, or alias for your new one.

I doubt you'll have to go past #1 above, though. That should be enough.

Edit: I read your original post backwards. The first thing you should do is make sure your path includes the new git directory BEFORE the directory that contains the old git.

You probably can just remove the definition of JAVA_HOME from .bash_profile and restart the shell. If you really need to set the variable, use

export JAVA_HOME=$(/System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java_home)

to define it dynamically depending on the installed JDK version or

export JAVA_HOME=/Library/Java/Home

to use the default place (which is symlinked to the above path).