Does the remove utility no longer work? I thought the remove utility still functioned, but that you could also set it up in BES Admin to run on a schedule if you wanted.
Here is some documentation on BES Admin tool options: http://www.ibm.com/support/knowledgecenter/SSQL82_9.5.0/com.ibm.bigfix.doc/Platform/Installation/c_list_of_advanced_options.html#c_list_of_advanced_options
You can use the REST API to delete a list of computers. This is how I typically do it.
Is this your RFE you filed on this? http://www.ibm.com/developerworks/rfe/execute?use_case=viewRfe&CR_ID=94726
If so, I have some ideas on how to automate the cleanup using the REST API and Session Relevance. How many computers do you typically delete at a time?