Move it don't kill it
As someone points out above, you can always shift something sideways (given sufficient room). My approach these days is to do something like
$ mv /opt/coolprogram /opt/was_coolprogram
The was_ prefix is sufficiently unusual that I can always find such "sidings" (backup is too strong a word) and remove them when I need the space, or I'm sure they're obsolete.
However, I'm not sure that would have worked on a running system with /usr. There's a lot of pretty essential stuff in that hierarchy.
Biting the hand that feeds IT
