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If /usr/bin/sage comes from a package install, it should disapear when the package that provides this file is removed. Hence, i bet that this binary comes from a depedency of sagemath, probably sagemath-common since /usr/bin/sage is a shell script hence architecture independent. So, you could let the distro remove that file by removing the trailing dependencies, by running apt-get autoremove.

Regarding your own compiled version of Sage, you should better symlink from /usr/local/bin to keep distribution-related and self-compiled software separated. This is also in the default PATH, so it will work the same, just a little bit cleaner.