You could do something like:
mv my-executable my-executable.bin
And create my-executable as a wrapper script that does:
#! /bin/bash -
{ time "$0.bin" "$@" 2>&3 3>&-; } 3>&2 2>> /tmp/times.log
The script could add more information to the log like the time it was started, by whom, the arguments it was passed...
BSD process accounting, at least on Linux does report CPU time (user + sys), though not in a cumulative way like time does (children processes CPU time is not accounted for the parent)