With "preferences/Advanced/Move deleted mails to trash and expunge immediately" *not* set, deleting a mail results in the internal message view being reopened if it was closed. It doesn't matter if you press DELETE in the folder list or while reading a message in the external message view.
Changes related to this bug have been committed. Please check latest CVS and update the bug accordingly. You can also get the patch from: http://www.claws-mail.org/tracker/ 2012-11-15 [colin] 3.9.0cvs6 * src/summaryview.c Fix bug #2785, "Marking mails for deletion reopens internal message view"