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It is auto installed with our root. No you cannot safely delete the .apk, and the only alternative I know of is superuser (although I cant really tell much of a difference between the two). IF you install superuser BEFORE you delete superSU, then you should be alright (although Im not sure if this is possible to do, I know uninstalling superSU/superuser is not the exact same as a regular app what with the binaries and all)
In SuperSU there is a option to switch apps hit that button then it will uninstall itself, download Superuser and open the app and update the binary and that's it