Mail indexes everything anyway. There's no turning that feature off. I just don't know what Mail will actually do, whether it will recognize the messages already there or not. If you fully migrated from Panther to Snow Leopard, it would probably remember, but it sounds like you imported rather than migrating, so you probably didn't capture any files that contained information about what messages had previously been downloaded. I also just haven't worked with a POP account in a long time.
So, here's an alternative, keep a copy of the imported messages in another folder. If they're in the Inbox now, select all and Option+drag to another folder. Then take your account online and see whether messages get duplicated. If they don't, great! If they do, you can delete everything and then move the backup Inbox back in.