Hi Nicolas,
I don't know how you (the team) sync the repository, but I find it easier to remove the old version and add the new at the same time.
I rsync the repository from andromeda into my local chroot sandbox, then I run 'makeworld', and then I rsync the modified repository back to the server. As far as I'm concerned, it doesn't matter whether I keep those old versions around or not, i.e. deleting the old versions doesn't simplify matters for me.
A way to mitigate this would be to either keep at kill list of files to remove and when and/or having a separate repo for these archives.
I believe the repo-clean utility http://code.google.com/p/repo-clean/ that Magnus mentioned could get the job done just fine. We could run that every 2 weeks or so to expire unused packages. It's not important to keep them around indefinitely, but I feel that we shouldn't delete them immediately at the time of an update either. Take care, Peter