Posix standards have nothing to do with Apple. /usr/bin/ is reserved for binary files delivered from the distribution. /usr/local/bin is available for administrators to add binary files which will not be touched by an update. If you wish to install in /usr/bin then it is YOUR responsibility to maintain the added binaries. MacPorts normally installs in the opt/local/ directory did you customize your installation?
For some reason /opt/local/bin was removed from my PATH. But yes, MacPorts was actually still installed in that folder.
I installed Git through the Command Line Tools installation from Xcode, so I didn't choose anything.
Nevertheless, I did not expect any update to remove anything I've installed on my system nor mess with my home folder without first warning me about it .