How can I prevent Mail from applying actions (moving/copying/flagging/marking read) to duplicate messages?

Question

I use Mail to check multiple accounts. When I receive the same e-mail in multiple accounts, actions applied to an e-mail in one account often (though not always) affect duplicate messages in other accounts.
Example 1
Someone sends an e-mail to both me and my wife. Mail is set up to check both accounts. If I open the message in my Inbox, it marks it as read in my Inbox as well as in my wife's Inbox.
Example 2
For historical reasons, I have chosen to have all my e-mail forwarded (by the server) to a second account, to be used essentially as an un-touched archive of all incoming mail. If I manually move a message from my main account Inbox to another mailbox, the destination mailbox will end up with 2 copies, one from my main account Inbox and the other from the "un-touched archive" Inbox (which has obviously now been altered unintentionally).
Does anyone know of a way to prevent this behavior. I can manage my own duplicates. I don't want Mail to do it for me.
(Btw, I already have the "AlwaysShowDuplicates" option set using "defaults delete com.apple.mail AlwaysShowDuplicates")

Answer 1

There are certainly many ways of organizing things so that Mail never has to deal with multiple accounts and duplicate messages (separate user accounts, separate computers, separate mail clients, etc., etc). That's just not what I was asking. I'd like to know how to fix Mail's behavior when it does have to deal with multiple accounts and duplicate messages.
I was hoping there might be another hidden preference or something (and by the way my original post should have said "defaults write com.apple.mail AlwaysShowDuplicates -bool true", instead of the "defaults delete ...")