Long ago Raphael blogged nice post how to delete expired updates from Configuration Manager 2007 http://wmug.co.uk/wmug/b/dotraphael/archive/2012/04/19/script-deleteexpiredupdates.aspx but script is not available to download now with current link.
This script is intended to remove all expired updates from a package or Deployment and was showed by the MVP Kent Agerlund on his presentation at MMS 2012 http://blog.coretech.dk/kea/mms-2012-simplify-your-deployments/
If you'd like to try (at your own risk), you can download it from here (just remember to remove _.txt to convert to vbs)
Examples:
cscript.exe DeleteExpiredUpdates.vbs /SMSProvider:CM01 /PkgID:"A010000E"
cscript.exe DeleteExpiredUpdates.vbs /SMSProvider:CM01 /AssignmentID:"1;2;3;4;5;6;7;8;9"
cscript.exe DeleteExpiredUpdates.vbs /SMSProvider:CM01 /PkgID:"A010000E" /AssignmentID:"1;2;3;4;5;6;7;8;9"