Unfortunately, no the BESRemover is not itself designed for direct automation. That’s not to say that you cannot utilize remote WMI calls to execute the BESRemover, but that would be custom and not directly supported.
Have you tried using the BESClient restart fixlet content from the BES Support external site before running the BESClient update fixlet content? You original error could be due to the BESClient PID being locked and a service restart can help.
If none of the above works for your specific situation, I’d recommend opening a support case with our L2 team.