There's usually no need to kill any processes, and doing so can corrupt config files or other data. The installer will restart Opus automatically in most cases (although see below), or you can tell it to exit in your script:
If Opus 12 was installed and Opus 13 then installed over the top, a reboot is required to update some of the DLLs to the new version. It may be that which is preventing dopus.exe from running after the 12 to 13 update.