you can set the server up to delete spam emails which have a spamassassin score of more that a specific threshold.
You can do this in server-manager/email/change email filtering settings/
then set "Spam sensitivity" to "custom"
"Custom spam tagging level" to (eg) 5
"Custom spam rejection level" to (eg) 12
then click "save" to apply the settings.
this will then mean that emails with a score over 12 will be deleted silently, over 5, will be retained, but either dropped into the "junkmail" imap folder and/or tagged with "spam" in the subject line. These are controlled by the "Sort spam into junkmail folder" option and the "Modify subject of spam messages" option.
Look in the wiki documentation for more details:
http://wiki.contribs.org/SME_Server:Documentation:Administration_Manual:Chapter13#E-mail_Filtering