As an alternative you can manually delete entries using a text editor, but you cannot delete the Log File itself. Depending on your versions of Mac OS X and Safari, you might find this log file in different places – I found mine at: Macintosh HD/Library/Logs/Console/501/console.log. If you use a utility such as Cocktail to automatically delete Log Files you should be okay, but be sure to check your log files periodically to be sure they are staying cleaned up.
If you’re not familiar with the Debug Menu, it’s a hidden feature of Safari that opens up a large number of Advanced User/Developer functions (in addition the the logging already mentioned), such as the ability to change the browser’s User Agent, Showing the DOM Tree and View Tree, opening the current page in one of your other installed browsers, and much more. The Debug Menu is not for casual users, but if you can make use of these features, all it takes is a single command line in Terminal to add the Debug Menu to Safari. First, be SURE Safari is NOT running, then open Terminal and type:
% defaults write com.apple.Safari IncludeDebugMenu 1
That’s all there is. If you ever want it gone, just retype the same line with a 0 in place of the 1.
I hope you’ve found this helpful! Let me know if you’ve come up with a different solution – I’d love to know about it.