You can script the following, or do it by hand for fewer users:
1) For each user:
a) do a omcpoutu for the mailbox
b) do a omshowu and store the details
2) Delete Scalix and create a new mailstore on 11
3) For each user
a) Create the user using the same data as in 1b
b) do a omcpinu from the file stored in 1a
And there you go
However, please note that omcpoutu does NOT store the mailbox rules, or MAPI properties (permissions on mailboxes, amongst others) at all, nor does it store public folders.
Also, this doesn't preserve the mailstore and its configuration at all. But it doesn't sound like you want that anyway. Just be sure to take a copy of any files you want to preserve (like smtpd.cfg, for example) and merge the results back into the mailstore.
Copying the whole mailstore is still the better route IMO, even if it can take longer to go from 9 -> 10 -> 11. Just note that Scalix 11 doesn't support FC4, but I am sure you know that.