You can unregister completely this view (even if the actual view is gone from the filesystem).
See "ClearCase: Is it possible to cancel checkouts not made from your own view?":
cleartool rmview -force -uuid (uuid_of_the_view) -vob \aVob
That will trigger, as a side-effect, the removal of the checkout status of any file checked out by this view (referenced by its uuid) in this vob (the -vob option).
See more at "How to delete clearcase views created by other users?":
cleartool lsview -l theViewToRemove # get its uuid
cleartool rmtag -view theViewToRemove
cleartool unregister -view -uuid uuid_of_viewToRemove
You even can use the nuke_view.pl script.
Now some of directories are obsolete and need to be rmname'd from other views, but this cannot happen apparently while they are still checked out on branch A.
As I mention  in "How do delete a file in ClearCase?", even if you don't unregister the view, you can still remove a file from a branch, even if it is checked out in another branch.
You simply need to do it from the command-line:
cleartool rmname -force /path/to/file
Eric Schnipke proposes in the comments:
- (1) cleartool lsview -l theViewToRemoveto get the view's UUID and then
- (2) cleartool rmview -force -uuid (uuid_of_the_view) -vob \aVobto remove the view and offending file version.