Well the current emails from POP3 are being downloaded to Outlook, so what you need to do is take the PST file from that email profile, connect the outlook to the Exchange server account using a new profile, and then you can either:-
1) import the entire PST to the outlook mailbox (make sure you up the limits on the mailboxes before you do this!, this gives them email history via exchange server, so OWA, OMA, activesync etc, and keeps everything nice and tidy on the server and desktop, but you might be importing a load of rubbish that would be better left out of your nice clean server.
2) the other option is just to take the PST file from the old POP3 profile and attach it as kind of an archive file, running next to the Outlook mailbox. So nothing new goes in there, but the user has it for reference. Of course this is not great for mobile users if you put the PST on the server, and its not good for backup purposes if you keep it local to the workstation.
On balance I would import the PST file into each users mailbox, probably the most elegant solution in the long run.