I was able to solve my issue.
First, the database size difference is not a problem, but rather a change that Apple has made to the mail database, so even a database with no records is about 313 MB to start off.
With respect to the cpu being hijacked, the problem for me was that the mailbox quotas were wonked. The way to fix the quotas (or quota roots, I think they're called) is by using the /usr/bin/cyrus/bin/cyrus-quota command with the -f option which fixes any errant mailbox quotas. once I did this, and restarted the mail service, the daily quota process became better behaved and syslogd also stayed under control. I guess there was something wrong with the quota roots. Since then, I no longer get negative numbers in the Server Admin > Mail > Maintenance >Accounts pane.
Hope this helps