If you're having problems deleting large messages in Webmail, try changing your settings so that your mail gets deleted directly, instead of going first to the Trash folder.

You set it up like this: log into Webmail and click on Options, then Folder Preferences.  In the Special Folder Options section, there will be a line for Trash Folder.  Change that to "[Do not use trash]" then click the Submit button at the bottom of the page (you'll need to scroll down to see it). 

This change tells Webmail to immediately delete any message that you click the Delete button for, instead of moving it to the Trash folder.  That should allow you to delete your messages directly, without causing problems with your mail quota.

When you're finished, you might want to change the Trash Folder option back to "Trash", so that you're protected in case you delete something accidentally.