I know that it is possible to manually disable or delete an agent on the Bamboo agents page. I am writing a Bamboo plugin that should delete Bamboo agents when the build is completed. There does not seem to be a straight forward way to do that either using the Bamboo REST API or SDK library.
We (Atlassian Build Engineering) are doing something similar in our plugins that we recently open sourced at https://bitbucket.org/atlassian/per-build-container
We create Docker based remote agents on demand, they build a job and then get removed.