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I wrote a test which confirms that the pathological branch rename causes a failure in the git-client-plugin checkout process when using command line git, and confirmed that the "git remote prune origin" command (and its matching setting in the API) resolve the issue.
I don't think we should change the behavior to always prune because that will likely discover users who depend on it not pruning. Those users who encounter the problem may choose to enable pruning of orphan remote branches, or they can wipe the workspace as suggested in this bug report.