Deleting of all workspaces in case you delete configurations should be optional. In large environment like we have there are some global workspaces on our build servers which are now being removed once a configuration is being deleted. This force deleting of all workspace should be an option which could be marked when you are going to delete configuration. Also I think that the deleting of workspaces should only be done in case the Workspace Directory Setting is set to 'Use configuration name to identify workspace directory' and not in case you make use of 'Use specified workspace directory'

For example:
On Windows node we have generic path to avoid path length problem with VS build, so therefore we make use of 'Use specified workspace directory" which is similar for each SCM repository where we build the Windows target.