Hey,
I really shouldn't be replying since I don't really know much about this, but since there are no replies yet I'll try to kick things off...
It seems like your using IMAP to access your mail (if you choose .Mac as the account type in Mail this is what its called), which none of my mail servers support, so I don't think I'll be of much help, but in the rule does it say to "copy" the message or "move" it? Moving could possible take if off the .Mac server and place it only on the computer that you checked it on.
If you use "copy" message on both computers as a rule, hopefully then if you check your mail first at work it will leave it on the .Mac server, and when you come home and check your mail it will hopefully think its new and the rule their should also copy it to it's hard drive.
Then hopefully it would just be a matter of deleting the older e-mails off .Mac (probably best to wait until the messages are around a week old to make sure both computers have them)
There is 15MB of storage with .Mac, and what your trying to do is basically the whole benefit of IMAP-- that you keep your mail on the server so you have it wherever you go.
Hopefully someone else will have a more concrete solution to help you
Ryan