The Pending queue is populated long before the email is even opened or deleted on the user's email client. Think of the BES, at this point in the delivery, as a mailman. Once he's already on his route, there is no real way of phoning him up and telling him not to deliver something because the person already came to the Post Office to pick it up.
As for the PST file, the BES would not recognize the email being filed away in the user's Personal Folders. This is due to client limitations of the service account - it simply does not have permissions to scan and view the Personal Folders (just as you wouldn't as an administrator of the Exchange server). It can only synchronize what it has access to. The users may not understand this, but as an administrator, you should. Alternatively, you can go to Intellisync in Desktop Manager then to the PIM settings for Email and there is a wired sychronization of the Personal Folders - but there is not (and likely never will be) an option for wireless synchronization of this configuration.
I believe there is a place where you can set the length of time the server holds pending messages before they expire, although I'm not sure where that is or if it exists (would make sense to have, and I believe I read about it, but who knows).
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