Was the error with SpamAssassin's config, or are the messages flawed somehow?
You can just split the file out into individual messages and resubmit them for normal delivery by piping them to
sendmail -t (an alias to Exim on a system with Exim set up as the primary MTA). However, if the messages are problematic somehow, that won't necessarily get you anywhere. Also, if messages were originally sent to a mailing list or the like, this will resend them out to the 'net, which is undesirable.
Another option is to use Python's
mailbox module to read in the mbox file and then manually drop the messages into the appropriate spools yourself; it supports most common formats. Given sufficient details, I could edit in some decent example code here.
(Python would work to split the messages out for submission too, though I'm sure a search will turn up a few dozen reasonably robust scripts for that kind of task.)