So many questions about this one.
Why would something by in /usr/bin that would be manual deletion? Wouldn't it be in /usr/local/bin? Were they manually deleting a package managed binary?
For that matter, if you're manually installing a component like node with a large set of dirs and you might want a different version at some point (you're more likely to update to a newer major version of node than you are some base library for the system) why wouldn't you put it into /opt/node-X.Y.Z (if not an actual package for the distro)?
We could assume the people weren't as much admins as devs with some minimal admin experience so weren't familiar with some of these common admin practices that have been developed over the years to manage stuff easier and safer, but then why are they root with the ability to blow out /usr/bin and not a user account installing node locally?
It feels like there's some larger problems that even allowed something like this to happen. It's like hearing someone say "my simple webapp connected to the wrong DB server and completely deleted out all the databases there, including the billing one." The first response I have to something like that is "what were you guys doing that something like that was even possible?"