If I recall, yes you can extract the mailboxes into pst files while the server is up, of course the mailbox owner cannot be in their mailbox while you are running exmerge.
But exermerge'e purpose is not as a backup tool but as a tool to move a mailbox say, or remove a mailbox.
You should be looking at a tape backup solution (depending on the number exchange mailboxes and servers you have) from Veritas-Backup Exec, Commvault-Galaxy or Computer Associates-Arcserver, to name a few.
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